Digimon - Digital Card Battles
Digimon Rumble Arena
Legend of Dragoon
Ragnarok
Toribash
Counter-Strike
The Sims
Final Fantasy Tactics Advance (Only GBA Game I actually played)
Monster Rancher 4
Viewtiful Joe 2
Okami
Shadow of the Colossus
GunZ
Lineage 2
Roblox ( i've been banned from it after i sweared at somebody who destroyed my whole map...)
Phun
Burning Sand 2
Harvest moon ( game for gameboy)
Call of duty 2
PC:
Syndicate Wars (never liked the original much, but I loved this)
System Shock 1 & 2
DOOM
X-Com (UFO Enemy Unknown)
Modern:
N/N+
Portal
Toribash
Fight Night especially needs a mention. The AtariXE version is a ancestor to the modern console versions. It obviously was very different back then, but had an epic create a boxer mode. I spent many, many hours on that game.