Only three
that may be a little hard considering it's not entirely fair to compare across genres.
1: Deus Ex
BEST GAME EVER - PERIOD.
This coming from someone who pretty much hates any singleplayer FPS. Sure it wasn't a straight shooter FPS, but I avoided all shooting games with a first person perspective for years. I somehow avoided HL1, never heard of the game until a few years later when apparently it was the greatest game ever released according to its review scores. For some reason I was "wasting" my time playing apparently not greatest games such as BG1 and 2, Planescape Torment and Fallout... when I should have been playing HL1 ... NOT :P.
Why Deus Ex? - the complete freedom and the fact that it was sci-fi. I can't believe I only played this game at the end of 2005. I had it for years, tried it in the beginning, didn't give it a chance at first, oh how stupid was I. I honestly regard this as one of the pinnacles of gaming.
2: Fallout 2 & Planescape Torment and Baldur's Gate Series
I have to stick all these three in at #2. It wouldn't be fair for me to choose one over the other. I have slightly more affection for Fallout 2, but that is primarily because of its setting. Post apocalyptic setting > fantasy for me, but I enjoyed all these 3 about the same. They also happen to be my favorite RPG's of all time.
Fallout 2 -> Guns, gore and twisted humor
Planescape Torment -> story and characters
Baldur's Gate -> epic, unique and beautiful
3: Grim Fandango, Broken Sword 1, Zork Grand Inquisitor and The Longest Journey
My all time favorite adventures. Story, characters and an empty feeling inside after completing each of them. Beautiful, beautiful games.