Yeah, I imagine some of these are just region locked or very tiny differences or in the case of the EA stuff exactly the same in most cases. Some like Marble Madness are completely different to the point of being virtually different games (EA's one being more like the computer ports with bad sound while Tengen's JP is almost arcade perfect or at least very very close) though. Of course there are probably more differences than that but it is the case of what you know and won't mention the Sonic games since they are quite known in terms of changes.
The ones that I can name off the bat:
Shadow of the Beast JP has different (better) graphics for Aarbon and some of the enemies/bosses, some of the enemies that aren't changed had a different palette or a very minor change (as in a few pixels). The sprites can be found here: http://www.spriters-resource.com/gen...ast/index.html That version also has an option screen with a sound test/number of lives. Oh and it is NTSC fixed compared to the US/EU version where it was designed for PAL but EA (the publisher) having one cart to fit most regions deal and over saw the 50Hz/60Hz difference. The JP version was published by Victor.
Virtually different games:
Dr. Robotnik's Mean Bean Machine/Puyo Puyo (same engine)
Marble Madness (JP, Tengen/M2?)/Marble Madness (US/EU, EA) [different programmers]
Magical Hat/Decap Attack (same engine with tweaks)
Klax (US/EU, Tengen)/Klax (JP, Namco) [different programmers]
Copyright/publisher changes:
RoadBlasters (U) credits Sterling Silver Software while RoadBlasters (JP) credits Lee Actor/Dennis Koble. Interestingly the RoadBlasters cart has a language/region setting so JP/NTSC = Japanese/Mega Drive, US/NTSC = English/Genesis, EU/PAL (not released) = English/Mega Drive (not sure about the last one though, have to recheck that one).
Fire Shark (U) credits Dreamworks, (JP) has the Toaplan logo and the EU version has no logo but the Dreamworks logo is in the ROM unused.
Rolling Thunder 2 and Talmit's Adventure (Burning Force as well?) credit Sega Enterprises Ltd. in the EU version.
John Madden Football (JP) is actually John Madden Football 92 but changes the copyright to EA Victor, changes the credits to include the "localised" staff and removes both John Madden's head (still in ROM though) and his message saying that he made an another Genesis game.
Winter Olympics (JP) removes the For Sega Mega Drive/Genesis message at the copyright screen and has some slight bug fixes (placebo effect?) but still is a terrible game with decent music.
Nigel Mansell's World Championship is credited to GameTek (U) and Konami (EU). As a result, the game starts differently between the two versions. In the US version, the Williams F1 car drives past the Sega logo then the copyright stuff but in the EU version the Konami screen starts first but can't remember if the car driving scene is still in or not after that.
Gain Ground (U) is credited to Renovation instead of Sega.
Mega Turrican (EU) is credited to Sony instead of Data East and as a result, the Presented by Data East voice is unused/removed.
Crack Down is credited to Sage's Creation on the title screen in the US version.
Graphic changes:
Marvel Land JP Prince Paco is more closer to the original arcade version while in the US/EU version (Marvel Land/Talmit's Adventure) Talmit has changed his hair for some reason. Also the title screen is different in all regions (JP = the same as the arcade, US = different, EU = completely different due to the name change).
Alex Kidd in the Enchanted Castle (JP) when you lose in a Janken match, Alex Kidd gets naked with only a leaf covering his privates. Since child porn is a big no-no in the US and the EU, instead he gets crushed by a ton weight. Unknown whether the Korean version is the same as the Japanese version or the US/EU version.
Cool Spot removes the 7up logo on the intro in the EU version.
Boogie Woogie Bowling (JP) has anime style portraits while Championship Bowling (US) has more realistic portraits. Also the US version changes copyrights to Mentrix Software.
James Pond II: Codename Robocod (JP) has a nice title screen instead of just text.
Rocket Knight Adventures (JP) has a different opening cutscene with a village getting attacked instead of Sparkster on a mountain and the Stage intros have an opossum band playing instead of a Sparkster portrait. Also I think there are also some difficulty changes between the 3 versions.
Other changes:
Asterix and the Great Rescue has some minor changes between the US/EU versions but sadly both versions feel like an early beta. The US version has theme names (e.g. Gaulish Village) that only appear one per stage but a shorter opening story. The EU version has a strange level name system (e.g. Level 1, Hut 1, Room 1) that appears on every stage and a slightly longer opening story. Also on the first Rome stage (Level 6, Hut 1-Room 1) has some minor level layout changes, there might be way more... Anyone who decides to cover this game in the beat all the US Genesis games thread has to make sure that it is the US version due to these changes.
DJ Boy (JP) has an intro, cutscenes and ending that were removed in the US/EU versions presumably due to ROM space. Also the Black Momma boss who farts was altered and censored to a White Woman throwing pies.
Super Airwolf (JP) has the Airwolf theme playing, while Cross Fire (US) has a different tune for the helicopter part in game and altering the music during the stage select, calling the character Billy (I think) and a different image in the Briefing Screen.
World Heroes (Asian version incorrectly called JP), the Player Select has a black background with the World Heroes logo instead of just blue in the US version. Also the MVS difficulty has been removed and replaced with a sound test. Sadly there are no other improvements in that version, no missing defeat hair loss portraits and the gameplay is the same.
Superman (EU) has a Virgin Games logo, includes a Options screen with a difficulty select/lives/Sound Test and removes the Sunsoft logo in the first stage (but is still in the ROM).
Speedball 2 (U) has horrible sound and only one song in the game, the (EU) and (JP) versions have music done by Matt Furniss with extra music. Apparently the JP versions also has palette changes but can't confirm.
European Club Soccer has club teams from Europe (e.g. Manchester United), World Trophy Soccer changes it to have world teams (smaller selection?) and J.League Champion Soccer has teams from the J.League (smaller selection?).
Streets of Rage II/Bare Knuckle II (EU/JP) has Blaze showing her panties during a jump kick. When the cart is set to JP mode, it also has Mr. X smoking and Skate is known as Sammy. Streets of Rage 2 (U) changes the logo and censors Blaze's jump kick.
We all know that Bare Knuckle III is better than Streets of Rage 3 (censorship, altered story, difficulty increase, changes for no reason).
Grand Slam: The Tennis Tournament 92 (JP) automatically has male players selected by default (pressing right goes to female), while Jennifer Capriati Tennis and Grand Slam (EU) default to female players (pressing left goes to male). The order is also slightly different with J. Capriati being no.1 in the US/Eu version while she is no.10 in the JP version. Since Grand Slam JP is in Japanese, I don't know any other changes but the players might have proper names? (one of them looks like Andre Aggasi) Oh and US version has a different title screen.
Prince of Persia (U) is more closer to the original version while Prince of Persia (EU) has an extra cutscene, music in game and different layouts. I think the EU version also has extra stages too.
Havoc (EU) starts at the pirate ship stage instead of the Green/Emerald Hill type stage in High Seas Havoc (U)/Captain Lang (JP), as a result the EU version has one less stage in the game normally (the stage is still there but disabled). Also adds the Codemasters copyright screen as well (I think).
Andre Aggasi Tennis (U) has an option screen that is not in the EU version, a different title screen and slightly different music. Basically different presentation but still the same game.
Super Masters Golf (JP) does not have the Fantasy Zone minigame that is in Arnold Palmer Tournmanent Golf (US/EU). Instead it has a scribble drawing.
Castlevania: The New Generation (EU) has censorship with blood being replaced by water in the title screen, Eric Lecrade's death animation is altered and the zombie enemy being palette altered. Vampire Killer calls John Morris, Johnny Morris.
Zombies (EU) has censorship compared to Zombies Ate Our Neighbors (US), one of the enemies got changed from a chainsaw maniac to a lumberjack and changes copyright to Konami.
Identical (from what I know):
Indiana Jones and the Last Crusade
Sonic Compliation/Sonic Classics (except one version of Sonic Compliation has a region lock, that's it)
Not sure:
Either OutRun or OutRunners have a strange title screen related bug that got fixed in the Japanese version. Can't remember...
Comix Zone (JP) is slightly easier? I know that it has both the Japanese and the English text in game while the US version only has English.
Super Monaco GP II (U) is just a region lock
Super Monaco GP (US) is just a region lock compared to its original World release.
The only differences between The Chaos Engine and Soliders of Fortune are a different title screen and the EU version has Options (that don't seem to work).
Also in Head-On Soccer/Fever Pitch Soccer, the cartridge has both names depending on region.

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