1. The Elder Scrolls: Daggerfall
2. The Elder Scrolls: Arena
3. The Ultima series
Games that are almost top 3:
4: Thief: Deadly Shadows
5. Deus Ex

top 3, I've got too many that i love, well how about
Obsidian
Zork
MechWarrior 4 Mercenaries

-Deus Ex
-Planescape Torment
-Operation Flashpoint

-Fallout 2
-Operation Flashpoint
-The whole Total War Series

Mechwarrior 2
Total Annihilation
Planescape Torment
and probably another 30 that could pop up based on my mood.

1 Tie Fighter, the best Dog Fighting space fighter ever
2, Little Big Adventure, Twinsen I miss you
3 Might & Magic 7
4 Transport Tycoon Deluxe
5 Fatal Racing (I played it for 2 years every day against my Friends).

Sucks...so many good games, so little ranking:
1) System Shock 2
2) Fallout 1
3) Planscape: Torment
Other noteables:
Deus Ex
Thief 1
Elder Scrolls
Baldur's Gate(s)
Half-Life

I won't list any of the games already on GOG, although there is definitely at least one that will be left out because of that.
1. Syndicate (Bullfrog)
http://en.wikipedia.org/wiki/Syndicate_computer_games
2. X-COM: UFO Defense (MicroProse)
http://en.wikipedia.org/wiki/X-Com
3. Populous (Bullfrog)
http://en.wikipedia.org/wiki/Populous
Oh, I would like to add one honorable mention. A game that could be better, but I loved it all the same...
- Shadow Company: Left For Dead (Sinister Games)
http://www.gamespot.com/pc/strategy/shadowcompanyleftfordead/index.html

In no particular order
Duke Nukem 3D
Deus Ex series
Zork series

1. Ultima IV
2. Civilization II
3. Oblivion

1. Deus EX
2. Baldies
3. Carmageddon

1. Half Life 1
2. PlaneScape: Torment
3. Elder Scrolls 3: Morrowind

Elder scrolls 4: Oblivion
Elder scolls 3: Morrowind
Baldurs gate 2

1. half life 1
2. half life 2
3. battlefield 1942