Japanese	American
At the character select screen, Strider Hiryu has different logos depending on which version is being played. Mega Man is known as Rock Man in Japan.

Japanese

This win pose of Morrigan's, which features Morrigan in a very revealing dress and Lilith chained up, is only in the Japanese version. Thanks to Jiterdomer for this info.

The announcer says a couple of names differently at the character select screen. The technique added to this game where you call both of your characters on and control them at the same time has a different name depending on the version. Mega Man/Rock Man's uppercut special move has him yell "Rock upper!" in the Japanese version and he just makes a generic grunt in other versions:

NOTES

-If you win a fight with Mega Man or Roll, sometimes Dr. Light appears in his win pose. In the Japanese version, Light actually speaks in Japanese, either congratulating his creations or offering them cake. His lines were removed from other versions of the game. Strangely his lines were restored the American and PAL versions of the Playstation port.

-Mega Man also has a win pose where Roll runs on with flowers and says "omedetou, Rock" (congratulations, Rock) in the Japanese version -but her line was cut out of other versions of the game. Thanks to Tiago Ueno for this.

-Roll's theme has lyrics in the Japanese version, but the lyrics were removed from the other versions of the game.

-Captain Commando has a move where he can call on one of his three team mates to perform an attack. In the USA version, he will just say "Come on!" when he calls a team mate on. However in the Japanese version he actually calls the name of his teammate out (Sho! Jennety! Hoover!). His teammates have different names in the U.S. version (Sho, Jennety and Hoover are known as Ginzu, Mack and Baby Head) so maybe Capcom forgot to get Takashi Nagasako (Captain Commando's voice actor) to also say the USA version names. Thanks to Mighty Kombat for this info.

-In the Darkstalkers series, Anita had her named changed to Amanda. However she's still called Anita in the American version of Marvel Vs. Capcom.