1. Bioware (Baldur's Gate 2 is the best WRPG ever IMO...)
2. Capcom (Resident Evil 4, Dead Rising.. I can't wait for RE5)
3. Epic (Unreal Tournament 99 is the best online FPS ever IMO...)
Honorable mention: Bethesda, Oblivion was very good and if Fallout 3 lives up to that (or even surpasses it) then it'll move them into my top 3.
ps. sorry I didn't use Nintendo, Square Enix, or Namco, but between those I'd pick Square Enix for first place solely for their Final Fantasy series. I haven't really gotten into a Nintendo game and really enjoyed it since the SNES days.