Only three... Dang this is going to be hard. :D
1. Baldur's Gate II
2. X-COM UFO Defense
3. System Shock 2
You're still getting a list of other games of my favorites: Portal, Jedi Knight series, Neverwinter Nights, Clive Barker's Undying, Half-Life, Half-Life 2, Call of Duty, Duke Nukem 3D.

My top 3 looks like that:
1.Vagrant Story
2.Civilization IV
3.Fallout
but there are many classic games that I missed (hopefully GOG will help me ;-) ).

Civ 2
System Shock 2
Deus Ex

3 just isn't going to cut it, so I'll start with these:
Harpoon
Mig 29 (You fly like a farmer!)
Starfleet Command
More later :)

Final Fantasy VI
System Shock 2
Final Fantasy Tactics

Planet's Edge I cannot believe that people who loved Star Control would fail to mention this great game. This is one game I really hope makes it to this service.
Darklands
Railroad Tycoon
As others have mentioned I could add a lot more. :)

Diablo II
Rise of the Triad
Duke Nukem (s)
Lowang!
Sin
Dues Ex / Dues Ex 2
Doom

- Baldur´s Gate 2
- Diablo 2
- Dune 2
- Neverwinter Nights 2

Definitely have to go with the following:
1. Legend of Zelda: Ocarina of Time
2. Final Fantasy VI
3. Rayman 2

1. Fallout
2. Planescape:Torment
3. Ultima 7: Serpent Isle

1. FFVII
2. Fallout 2
3. Half Life

What just missed out on making my list.
Red Alert - Great game but its just not got much replay value for me.
Duke Nukem 3D - Classic game but there are some floors there
X-Com: UFO Defence -Great game but it just lacks something.

1 - Duke Nukem 3D (Name me a game before this, where you could meet an enemy taking dump on a toilet, killing him while he's sitting there, taking a leak in the toilet, then flushing it, after whis you break it and drinkthe pipe water... The fact that you even get health or taking a piss and driking water makes it just the more rewarding being so destructive... Interactivity rules, wish i saw more games these days with crazy stuff like that... Something simple like a light controlling switch on a wall is hardly seen in todays games... Duke 3D had great gameplay, Duke's character is pure badass-tastic as well)
2 - Carmageddon (Racing around freely, running over them pesky pedestrians, making it more laughable using powerups, and destroying your opponenets, all fun times... he soundtrack was great as well)
3 - Alien vs Predator Gold (The skirmish mode is seriously awesome, nice time killer)

Tricky question! The best I can do is my top three on specific platforms I've owned over the past 25+ years of gaming:
Sinclair ZX Spectrum:
Lords Of Midnight
Elite
3D Starstrike (excellent clone of the original Star Wars wireframe arcade game)
Commodore Amiga:
Deuteros
Dungeon Master
Speedball 2
PC:
Galactic Civilizations 2
Duke Nukem 3D
Heroes Of Might & Magic 3

1. X-com: Terror from the Deep
2. Rocketz
3. Day of the Tentacle

1. Freelancer
2. Portal
3. Half-life