Having played every game in that list, I've still got to give the nod to GTA:SA.
MGS3 was amazing, but that damn Snake Eater theme song.... <shudder>.
I never really played GTAIII and GTA:VC. GTA:SA was the only one I ever bothered to beat. Great story, perfect pacing, and lots of extra activities.
And no WoW on this list? I know I co-nomiated it; don't know if that was good enough.