References are for the Italian editions! Your books could be different.
Click on
to watch the described image.
I'm sure every Shirow's fan has recognized some of his oldest characters in new series. Sometimes it's easy to see it, other isn't. In this page I have tried to list every crossover I have found; obviously there could be more, so please mail me if you know crossovers you don't see here! Thanks.
References are for the Italian editions! Your books could be different.
Click on to watch the described image.
Some words about Black Magic. It's the first manga by Shirow, so there are a lot of situations and characters developed in other works (in particular Appleseed). I'm not sure about listing some of them in Crossovers, so I prefer to make a brief note: the use of Greek names; a super computer (named Nemesis or Gaia) who controls the Earth; bioroids; Duna Typhon and Yasha are the prototypes of Deunan and Hitomi (Shirow said it in Intron Depot at page 44); Captain Adams (the chief of the special forces who destroy the first two M-66) seems the Colonel of Appleseed; Hecatoncheires is the name of the robot used by Hermes against Duna and also it's the type of Briareos' cyborg body; the Commander, who wants to stop two more M-66 using the M-77, seems Brenten.
The first manga quoted for each character is where he has appeared for the first time. The chronological order of Shirow's work is: Black Magic (1983), Appleseed Book 1 and 2 (85), Dominion (85), Appleseed Book 3 (87) and 4 (89), Ghost in the Shell (89/90), Orion (91), Intron Depot 1 (92), Dominion C1 (95).
He is a little being, with a big head and huge black eyes. He appears sometimes as background character. [Really I have noticed him only at the end of my researches, so... help me!.]
Appleseed 
"26. Called Games" page 15 (middle; behind Norimochi and Kinako who have just knocked down Deunan). 
"26. Called Games" page 25 (middle; he is strolling in front of a building which is going to be inspected by Briareos and Deunan).
GitS 
"10. Brain Drain" page 13 (top; he is in the gallery of the Parliament).
Intron Depot 
He is in the cover for Machine Head 3 at page 110.
The Ghost in Machine Head 
He meets the huge squid at the end of the first story (click to know more).
Orion 
When the Naga explodes, we can see an Alien style octopus (the one with big black eyes).
Dominion Conflict 1 
page 71 (top; four aliens are going for a walk in Newport City while Suzuna, Makina & Rerika are patrolling looking for Superintendent Sakura's car).
GitS 
"07. Phantom Fund" page 12 (middle; he is speaking with the Puma sisters in Berutarube and he is bringing a Puma doll).
Dominion Conflict 1 
Toku, a member of the Tank Police scientific division, is certainly another great fan of Anna.
A sailor is reading Appleseed in the sand port.
"06. Robot Rondo" page 8 (top; an Appleseed T-shirt is displayed in the background just after Batou has destroyed an android; thanks to Luc).
Really this time he works as a waiter, anyway he is the hostage in the Midnight+1 Bar released by Leona.
"24. Stealth" page 2 (he is the barman in the café where "One Eye" Deunan goes into following the Israeli agent). 
"25. Shalom" page 68 (he speaks with Sokak just after Deunan has put a bomb on his car; he is quoted in the Data Book too, perhaps he is working for the English).
"02. Super Spartan" page 37 (top; in the café where Aramaki announces the creation of the special squad).
Shirow has used bioroids characters for the first time in Black Magic. They were distinguished by horns on their heads.
Appleseed 
"11. Zero Hour" page 1 (bottom; an "horny" character is going for a walk in Olympus before the parade of the Millepede platforms).
He is the chief of the Tank Police in Dominion.
GitS 
"02. Super Spartan" page 21 (middle; one of the cyborgs of the welfare institution security looks like Brenten; he is killed by Ishikawa).
They are the cyborg and the girl main characters of Appleseed.
Dominion Phantom 
page 9 (middle; there is only Briareos in the background while a guy is asking about Honest Luke's pension).
GitS 
"02. Super Spartan" page 9 (bottom; they are sitting on the stairs outside the van where are Motoko and Batou). "10. Brain Drain" page 13 (top; they are in the gallery of the Parliament).
Orion 
At the beginning when Seska has just arrived at the Sokoku Palace; they are very small (look at the bottom left corner) and difficult to find so I had to do an enlargement; thanks to Troy Murray.
Dominion Conflict 1 
page 71 (middle; on the sidewalk in Newport City, just before Suzuna, Makina & Rerika came upon a street fight; thanks to Lucas Loh).
He is the boss of the terrible Buaku Gang, which is lording it over Newport City in Dominion.
Appleseed 
"11. Zero Hour" page 2 (top; before the presentation of the Millepede Platforms, with other people from Dominion). 
"Appendix 2" (the short episode at the end of the second book) page 2 (top; he is on the stairs while the main characters are going for a walk and enter into an armory). 
"25. Shalom" page 64 (top; his face is on a wanted poster in Lance's office).
The Ghost in Machine Head 
In the first story he is among the escaping crew of the pirate submarine after it has been attacked by the giant squid. 
During the second part of the second story (top of page 3), Buaku and Crolis are competing for the food with Habana (click to know more).
Anyway I have seen them for the first time at the beginning of the Appleseed episodes inside Hypernotes. They get lost and ask help to Artemis.
Manmachine Interface 
"Dual Device 2" page 8 (top; only the male is inside the Paranodrome club while Motoko is speaking with the barman). 
"Dual Device 3" page 17 (middle; they are jammed in the traffic while Motoko is flying to Poseidon).
In Dominion she is the prototype of a new being (half human and half plant) created as the future inhabitant of a polluted Hearth.
Appleseed 
"11. Zero Hour" page 2 (middle; before the presentation of the Millepede Platform; above there are other people from Dominion).
The Ghost in Machine Head During the second part of the second story (top of page 3), Crolis and Buaku are competing for the food with Habana (click to know more).
Some of the funniest moments of Dominion Phantom of the Audience are Leona's quarrels with the demonstrators. In particular look at the people in the middle of page 8.
Appleseed 
"26. Called Games" page 13 (top; you can recognize some of them behind Deunan, just after her car accident).
GitS 
"06. Robot Rondo" page 9 (middle; at least two of the demonstrators for the rights of androids are the same seen in Dominion Phantom).
Dominion Conflict 1 
page 93 (bottom; back to their origins! Here they are protesting against Leona in front of Sagawa's factory).
Manmachine Interface 
Preview page 4 (bottom; here they are again, one of the last crossover added by Shirow).
He is one of the members of the Newport Police Department from the Dominion manga.
Appleseed 
"11. Zero Hour" page 5 (middle; he appears among the crowd who is witnessing the Millepede Platform parade).
GitS 
"03. Junk Jungle" page 16 (the two dustmen and their truck, one has been hacked by the Puppet Master).
Dominion OAV Act. 6 (they are escaping from Leona and her friend Charon during Leona's flashback about the time she spent in the motorcycle division).
Manmachine Interface 
"Dual Device 3" page 17 (bottom; they are doing their duty while Motoko is flying to Poseidon. Their faces are not visible, but in GitS the logo on the vehicle was the same).
They are all characters from Orion: Dr. Hebime is the military adviser of the imperial court; Eight Infernal Wizards (Arhat Vajra) have been evoked by Seska to fight against Susano; Lady Sakura is one of Kushinata's body-guards (the girl who has shorter hair).
Appleseed 
"26. Called Games" page 3 (bottom; at Midon train line exit, together with other people from GitS; really there are two Dr. Hebime).
Dominion Conflict 1 Only Dr. Hebime, page 71 (top; in Newport City while Suzuna, Makina & Rerika are patrolling looking for Superintendent Sakura's car).
He is one of the most famous and utilized Shirow's character. 
He did his first apparition in Black Magic as the creator of the M-77 robot (built to fight against the M-66).
Appleseed 
"6. Battle of Titan" page 11 (bottom; he succors an injured Briareos). 
"7. Rest" page 1 (bottom; in the hospital, he is slapped by Hitomi). 
"8. Alien" page 14 (in the garden of the hospital, he sells his book to Deunan). 
"15. Point Man" page 33 (top; among the crowd, in the background while Artemis is jumping pursued by Briareos). 
"18. Dead or Alive" page 50 (bottom; on the plane back from Benandanti Operation, after he has operated Hermann). 
"25. Shalom" page 57 (top; he succors an "one eye" Deunan after she has defeated the men who wanted to kill the Secretary General Boyle).
GitS 
"06. Robot Rondo" page 10 (bottom; behind Kusanagi, before she and Batou enter in the scientific division of the police department). 
"08. Dumb Barter" page 9 (middle; in the operating theater behind Kusanagi and her boyfriend).
Appleseed 
"17. Live Drive" page 1 (he is the scientist who has prepared Mumma's giant landmate).
Appleseed 
"26. Called Game" page 2 (middle and bottom; among the crowd in the train of the Midon line).
thanks to Oskari
He appears in GitS just after Puma Sisters (episode "07. Phantom Fund" page 12; bottom).
Dominion Conflict 1 
His name is Habana and he is Leona's Squad Corporal.
The Ghost in Machine Head 
The main character of these two short stories looks like Habana (click to know more).
Black Magic Appleseed
He is the character with a Zaku (the enemy mobile suit in Gundam) style head. He appears in many Shirow's manga and he is a fond of mechanisms.
Originally he should be one of Masamune Shirow's best friends since his first times in the world of manga (Black Magic published on Atlas Magazine); perhaps he was his assistant. His name is quoted on Intron Depot too (page 46). Often he appears together with another man with long hair and glasses. I think he is another friend but I don't know anything about him (* means the presence of both).
"Prologue, Expansion" page * 3 (bottom; they are sitting in the Onimal bar). 
"Battlefield: act four" page * 8 (they are part of a National Guard tank crew, who intervenes against the M-77). 
"Chapter 3, City Lights" page * 2 (in the Onimal bar aboard the colony star ship).
Appleseed 
"4. Hospitality" page * 12 (bottom; among the crowd). 
"8. Alien" page 38 (middle; inside the Onimal bar behind Hitomi and Yoshitsune). 
"9. Dominate the Mind" page * 2 (bottom; into the Parliament, he is sitting in the top row). "11. Zero Hour" page * 2 (top; before the presentation of the Millepede Platform, there are also characters from Dominion). 
"12. Battle of Tuphon" page 7 (middle; one of the Police landmates, who are passing over a traffic jam, has a single eye and very characteristic Zaku shoulders armor; thanks to Luc). 
"23. Outlook Envelope" page 5 (bottom; at a road block, behind his motorbikes while he is discussing with a Cottus Police robot). 
"25. Shalom" page 67 (top; in front the café riding his motorbikes, before the explosion of Sokak's car). 
"26. Called Game" page * 1 (top; they are under a beach umbrella looking at a sexy Hitomi. I think that one of the other guys is Shirow himself). 
"26. Called Game" page * 34 (top; on the floor under Mary's flat; over, there are Kitamura and the killer woman who is going to murder him. It could be Shirow's studio, so probably Hagane is one of his assistant).
Dominion 
Behind Leona and a policeman holding briefs; thanks to Maciej. 
Among the policemen who have surrounded the kidnapper after Bonaparte has demolished the Midnight+1 bar; thanks to Luc. 
* In the background of the deck of the sand track, just after the pursuit between Bonaparte and the Puma Twins. 
Behind the Tank Policemen who are watching a Puma girl transmitting from the space center after Buaku's escape.
Dominion Phantom page 9 (middle; in the background while a guy is asking about Honest Luke's pension).
GitS 
"09. Bye Bye Clay" page 21 (bottom; driving a motorbike outside the van where Togusa is doing a research about Dr. Willis). 
"10. Brain Drain" page * 13 (bottom; they are sitting in the first row in the Parliament). 
"10. Brain Drain" page 25 (middle; in the background of the howling special board of inquiry).
The Ghost in Machine Head 
* In the first story, they are among the crew of the pirate submarine; Hagane seems to be the lieutenant of the captain. 
* During the first part of the second story, they appear in a small drawing at the bottom of the fourth page (click to know more).
Orion 
* At the beginning, outside the pub where Seska his having a party. 
After the birth of the Nine Head Naga, he appears two times among the crew of a ship commanded by Dr. Hebime. 
He is one of the monsters who are trying to catch Susano while he is wandering inside the Naga (note the big nib); thanks to Luc. 
When the Naga explodes, we can see a Zaku style octopus (in the middle of the same page where are raining octopuses)!
Dominion Conflict 1 page * 71 (top; in Newport City while Suzuna, Makina & Rerika are patrolling looking for Superintendent Sakura's car).
Manmachine Interface 
"Dual Device 5" page 14 (top; in the cyber-space, Motoko's enemy is checking some personal files. One of the faces looks like a Zaku).
They are all characters from GitS: Hanka doctor and Colonel Tonoda come from "06. Robot Rondo"; Koil Klasnov is the Soviet killer in "07. Phantom Fund"; the Prime Minister appears in the episode "10. Brain Drain" (page 41).
"26. Called Games" page 3 (bottom; at Midon train line exit, together with other people from Orion; really there are many Prime Ministers).
He is the fat Home Secretary of GitS, the minister who speaks with Kusanagi after the murder of the Soviet ambassador ( 
"01. Prologue" page 8).
Orion 
At the beginning, when Seska is having a party in the pub. He is the man lain down on a table, under a singing Seska.
"07. Phantom Found" (page 18). He is an old "friend" of Kusanagi.
Orion 
He is one of the Eight Infernal Wizards (Arhat Vajra) evoked by Seska.
Appleseed "26. Called Game" page 3 (bottom; at Midon train line exit, together with other characters from GitS and Orion).
GitS 
"07. Phantom Fund" page 12 (middle; it's the earring used by a man in Berutarube).
Orion It's the insignia of the Kewpie pub where Seska is having a party.
Appleseed 
"26. Called Game" page 32 (bottom; she is the woman who murders Kitamura).
Dominion OAV Act. 5 (she is the Major of Newport City).
Appleseed 
"16. Life Point" page 8 (bottom; the name is written on the shoulder of the landmate built by Yoshitsune).
They appear only one time at the beginning of Dominion - Phantom of the Audience.
Appleseed 
"21. Decoy" page 24 (middle; near Hitomi and Yoshitsune just before the concert and the assault by the Mumma landmate).
Appleseed 
"12. Battle of Tuphon" page 18 (bottom; on the sign over the entrance of the underground; during the escape from the Millepede platform).
GitS 
"07. Phantom Fund" page 7 (bottom; it's the name of the train used by the Russian killer Klasnov to arrive at Berutarube).
It's the runaway robot of Black Magic.
Appleseed 
"16. Life Point" page 22 (middle; in the ESWAT mess after the meeting for the Benandanti Operation).
I'm not sure, but perhaps he appears inside Orion. He is wearing the uniform of the Yamata soldiers; he has a big nib and some comic pages; thanks to Luc.
Perhaps he also appears inside Appleseed, together Hagane Kotetsu.
"03. Junk Jungle" page 2 (top; it looks like a small spider, but he is equal to the deformed version drawn so often in Appleseed).
Dominion Phantom, Dominion Conflict 1 
Leona works for the "Newport Police Department" [I haven't found any reference to Newport in the original Dominion].
Black Magic Shirow: "the man likes so much the punk style that to comb his hairs he uses sugar lumps even if he hasn't to eat, because he must live using the strict essential. They are only background characters, so their punk style isn't so rich."
Appleseed Appleseed GitS
Perhaps this names are meaningless to you, but I'm sure you know them. They are the boy with punk hairs and sunglasses and the girl with ponytail hairs. They are the first "notorious" Shirow's characters to appear.
"Prologue" page 3 (bottom; among the crowd). 
"Prologue" page 15 (in front of the Onimal bar, struck by Kongoki). 
"Battlefield: act four" page 17 (M-77 breaks a wall after the evacuation of the building). 
"Chapter 3, City Lights" page 22 (struck by the runaway Hermes).
Appleseed 
"11. Zero Hour" page 11 (top; among the crowd). "Appendix 2" (the short episode at the end of the second book) page 2 (top; they are leaning out a balcony while the main characters are going for a walk and enter into an armory). 
"16. Life Point" page 5 (middle; only the heads behind the banquet). 
"21. Decoy" page 11 (bottom; at the end of the stairs when the Mumma's landmate is pursued by SASAM missiles). "26. Called Games" page 13 (they crash into Deunan's motorbikes).
GitS 
"05. Megatech Machine" page 6 (top; sat down in the café in front of Motoko). 
"08. Dumb Barter" page 18 (bottom; in another car during the car chase). 
"11. Ghost Coast" page 7 (middle; on the truck when arrives the thieves).
Orion 
At page 81 you can see two little Norimochi and Kinako under a flying battleship of the Yamata Empire.
Dominion Conflict 1 
page 71 (top; they are going for a walk in Newport City while Suzuna, Makina & Rerika are patrolling looking for Superintendent Sakura's car).
At the beginning of my researches I didn't want to include the famous Shirow Octopus, then I have changed my mind but it was too late. I'll add its apparitions as I'll found them (help me!).
"26. Called Game" page 48 (bottom; he is swimming, while super deformed Briareos and Deunan are enjoying the seaside; thanks to Luc).
Dominion 
In the same picture where Leona shots Uni (her helicopter becomes a motor bike) there is a man wearing a jacket with the inscription "octopus army"; thanks to Luc.
Dominion Phantom 
page 3 (top; behind the District Prosecutor who is shooting at Bonaparte).
GitS 
"07. Phantom Fund" page 12 (top; as sign of a stall in Berutarube). 
"11. Ghost Coast" page 11 (middle; on a sort of UFO while the Puppet Master is speaking with Motoko).
Orion At the end, the Naga explodes in millions of octopuses.
Dominion Conflict 1 
Too many to tell you where they appear. Basically the octopus will stick on anybody's head when they make a fool of themselves. Leona holds the record for having 3 octopus stacked one by one on her head.
Manmachine Interface 
"Dual Device 2" page 6 (middle; near the girl at the entrance of the Paranodrome club).
It's the bar managed by bioroids in Black Magic. It's reopened more times: 
in Teotihuacan City ("Prologue", page 15); 
in the main street aboard a sort of orbital star ship ("Prologue, Expansion", page 3); on the colony star ship ("Chapter 3, City Lights", page 2); 
on the planet Venus ("Epilogue" page 2).
"2. Civvy Street" page 30 (the Bar & Coffee House Onimal is Hitomi's home and the place where Olympus "guests" can rest).
He is the Pirate Edition (a Japanese manga magazine) logo.
"02. Super Spartan" page 36 (bottom; on the cover of a book while Togusa is thinking he must change work). 
"06. Robot Rondo" page 13 (top; printed on the T-shirt worn by one of the robots locked inside the Scientific Police Department).
Intron Depot 
At page 86 there is a Pirate Edition cover with a girl (obvious) and the Pig.
Do you remember the strange airplane used by the Yamata messenger to deliver Dr. Hebime's message to the Emperor Zokoku?
Appleseed 
In the episode "16. Life Point" at page 3 the drawing on the windows of the building seems that vehicle.
Appleseed 
"11. Zero Hour" page 5 (middle; among the crowd who is watching the parade of the Millepede Platforms).
They are Buaku's deputies in Dominion.
Appleseed "11. Zero Hour" page 2 (top; one of the characters, who are listening Buaku, seems one of the Puma; before the presentation of the Millepede Platform, together with other people from Dominion). 
"Appendix 2" page 2 (top; as one of the main characters of the Dominion series, the Puma sisters have deserved their personal café; in the same picture there is Buaku too; thanks to Luc).
GitS "07. Phantom Fund" page 12 (they are selling robot components in Berutarube).
GitS 
"03. Junk Jungle" page 41 (bottom; the artificial body used by the Puppet Master to contact Colonel Males).
Dominion OAV Act. 6 (the man, working for Dainippon Giken Company, who traps Leona and wants to change her personality).
She is the android used by GitS Section 9 as employed in coordination and controlling.
Appleseed 
"26. Called Game" page 45 (top; in the control room just after the arrest of the killer woman).
The brain of the chief has been hacked so he recognizes Motoko as the daughter of the Sagawa official photographer; the other man is in the control center with him.
Orion 
Look at the Man of Stone and the Man of Steel evoked by Seska to defend Kurama Tendai.
It's a weapon factory and Shirow's characters often use many different models. You can see them in Appleseed, GitS and Dominion C1.
Seska and her father Fuzen are among the main characters of the Orion manga.
Appleseed 
"26. Called Game" page 10 (bottom; they are at the bottom of the stairs, in front of the café where Briareos finds Mary. There are more Orion characters inside).
Manmachine Interface 
"Dual Device 1" page 30 (bottom; in the background behind two policemen).
They are among the main characters of Orion manga.
Appleseed 
"26. Called Game" page 11 (top; they are sitting in the café where Briareos finds Mary).
Appleseed 
"25. Shalom" page 36 (they appear during the fight between Briareos and Kainis' landmate; really I hadn't recognized them, but they are quoted in the Data Book).
GitS "07. Phantom Fund" page 12 (top; she is leaning against a stall in a crowded square of Berutarube).
Orion 
She is seated at the foots of Emperor Zokoku when Dr. Hebime's message arrives (he wants an attack against Susano).
"2. Shalom" page 68 (top; on the television at the end of the café where is Sokak).
He appears some time inside GitS. For example to announce the recovery of the Hanka administrator from the waters of the bay.
"15. Point Man" page 4 (bottom; the Guges MM landing from the flying vehicle have a smiling logo on their shoulders [unfortunately I haven't been able to read the words written below it]; thanks to Matsuyama). 
"21. Decoy" page 16 (middle; on the helmet of a Police landmate; the same landmate appear in the episode "6. Battle of Titan" but the words are a little different; thanks to Luc). 
"Appendix 1" (Yoshitsune is wearing a T-shirt with those words; thanks to Luc).
"03. Junk Jungle" page 37 (bottom; the bad guy, just shot by Togusa, falls down while a man is wearing a smiling we kill for peace T-shirt in the background; thanks to Luc).
He is the bad guy in the Appleseed OAV.
Dominion Phantom page 9 (middle; he is the guy who is asking about Honest Luke's pension).
In Dominion - Phantom of the Audience a "writer mouse" escapes from the fire of the Smartball Stadium.
Appleseed 
"4. Hospitality" page 12 (bottom; among the crowd).
Orion 
There is a "writer mouse" on the log which is going adrift just before the ending.
Appleseed "26. Called Games" page 15 (middle; behind Norimochi and Kinako who have just knocked down Deunan).
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