Off the top of my head, games that get a lot of play around my house:
~Side-scrollers~
Mame:
Elevator Action II, D&D: Shadows over Mystara (or whatever its called), Alien vs Predator
~Fighters~
Zinc:
Rival Schools, Street Fighter EX2 Plus
Neo-Geo:
King of Fighters (I prefer: 2003, 2000, and 2001), Samurai Shodown 4, Last Blade 2
Mame:
Street Fighter Alpha 3
Street Fighter 2
Dreamcast:
Marvel vs Capcom 2
Capcom vs SNK 2
~Scmups~
Mame:
19xx
Dreamcast:
Ikaruga, Under Defeat, Gun Bird 2