For me it has to be Balder's Gate 2. Best combination of story, tactics, atmosphere, etc in my opinion. Surprised I am not seeing this one more as peoples favorites.
Other favorites in no particular order would be Ultima 3 and 4 (never played 5 or 6), SSI Gold Box games, Wizardry 6 (went to scifi-ish after that), Morrowind, Wizard's Crown, Bard's Tale 1 and Vampire The Masquerade - Bloodlines. Although there were a lot of other good ones posted they just never stuck with me the way those did.
Currently playing Dragon Age at the moment and loving it. Can't say yet if it is good enough to one day make my all time favorite list but can tell I like it better than anything released in the past few years at least (Obvilion, Fallout 3, Mass Effect).