Alternate Color
When you select our fighter press and hold the 
button and you'll get that fighters alternate color. Doing this with Nakoruru gives you access to alternative winquotes since, traditionally, the palette swap is associated to her repressed aggressive side.
Cinema Mode
Press 
as the SNK VS Capcom logo appears.
Fast Character Select
Beat Tourny mode on Gamer difficulty.
Hidden Characters
To unlock Akuma, Yuri, B. B. Hood, Akari, M. Bison, Geese Howard, Evil Ryu and Orochi Iori you must beat Tourney mode, and you will see a silhouette of one of the characters covered by blocks in a 3 / 3 grid. Some of the blocks will be randomly removed depending on your difficulty setting and whether you defeat your rival between Stages 4 and 5 (whereupon you will be allowed to fight Evil Ryu/Orochi Iori) or not. When the characters are completely revealed, then you can use that character.
NOTE: block removal is completely random and may target previously removed blocks.
HINT: A faster way of doing this is exporting your VS. points (gained in Olympic events) to SNK vs. Capcom: Card Fighters Clash. If you've collected enough points to complete your card collection, when you link Card Fighters Clash back to Match of the Millennium, you'll have all characters unlocked.
Play as Fio in Target 9
Select Target 9 and then press before the GO sign comes up. You should hear the reload sound if you did it correctly.
Alternate Cat Walk Mode
Select Cat Walk and the select our song with . The arrow, A and B symbols will be replaced by a mouse, fish and a bell. Felicia will be in her alternate color as well.
Handicap Match
When playing in Team or Tag mode, you can play with only one (or two) fighters by pressing after selecting your characters.
Blood
To get blood in the game, you have to set your Neo Geo Pocket Color's internal language to Japanese.