In particular order
1. Thief series (I, II, T2X, and TUT)
2. Myst (all)
3. Sam and Max: Hit the Road
In no particular order
4. Heros of Might and Magic (II & III)
5. Battlefield 1942
6. Baldur's Gate (i & II)
7. Diablo I
8. Shogun Total War
9. Soldier of Fortune II
10. Perfect Dark (and by extension Goldeneye)
Honorable Mentions: Portal, Half-life (all), Toy Commander
Most are important to me not because they're better than others in technical ways, but if ever I could call some games mine, these would be them.

Hey everyone, just wanted to let you guys know that I made a top 10 PC games list for YouTube...
Check it out

Bump.
In order
1) Fallout 2
Not in order
HL1/2
KOTOR1/2
PS:T
SC3000
VtM:B
TTD
Nox
C&C:RA1

fixed

1. Ultima 7: The Black Gate, Forge of Virtue, Serpent Isle, Silver Seed.
2. Baldur's Gate inc. Tales of the Sword Coast, Shadows of Amn and Throne of Bhaal.
3. UFO: Enemy Unknown (aka X-COM: UFO Defence)
4. Quest for Glory 4: Shadows of Darkness
5. Space Quest 4: Roger Wilco and the Time Rippers
6. Diablo II inc. Lord of Destruction
7. Jagged Alliance 2
8. Crusader: No Remorse
9. SimCity 2000
10. Alone in the Dark
11. Command & Conquer: Tiberium Dawn (+Sun, but not C&C3, was v. disappointing!)
Whew. Had to cut a lot, was up at 17 games for a while, had to make some tough decisions! (and was still left with 11)

1. Battlezone
2. Heroes of Might and Magic Series, especially Part II
3. Warcraft II
4. Outcast
5. History Line 1914-18
6. Sword of the Stars
7. Hostile Waters
8. Crysis Warhead
9. Free Space II
10. I-War II

List of THE Games that I remember most fondly and still play sometimes.
Old games mostly - maybe because I was younger, or maybe 'cause they have that certain 'something' :), but those are games that kept me playing night after night - as well as doing many strange things, so my parents wouldn't notice :D
Nowadays it's not the same :(
01. TES II: Daggerfall (forever and ever - I have a DOSBox shorcut even now)
02. Terminal Velocity (my 1st mouse steering = immersive flying experience)
03. Thief 2 (if you don't understand no explanation will help :) )
04. Betrayal at Krondor
05. World of Xeen
06. Heretic (I guess playing it, (and Doom) at such young age was a mistake... [insert generic Evil Laughter])
07. Neverwinter Nights (thanks to mods only)
08. Might & Magic VII (I have whole notebook filled with painstakingly made maps, charts and notes for this game)
09. Dungeon Master II
10. Lemmings (for being Lemmings)

Mine aren.t in order because it's like picking a favourite child. Also because I'm lazy. Mostly the lazy.
-Prince Of Persia: Sands Of Time (dripping with style)
-Mafia: City Of Lost Heaven (dripping with style)
-Syndicate (dripping with style and the blood of innocent civilians who got in the way of 4 miniguns)
-Warhammer 40000 Dawn of War
-Discworld Noir (there goes that style again)
-Grim Fandango (ditto)
-GTA4 + The Lost & Damned expansion
-Wizball
-Paradroid
-Silent Hunter 3

Close/Interchangeable: System Shock 2, Another World/Out of this World, Arcanum, Half-Life, Half-Life 2, Jedi Outcast, S.T.A.L.K.E.R.: Shadow of Chernobyl, No One Lives Forever, Metal Gear Solid IV, Grand Theft Auto: San Andreas, Gothic, Shenmue, Super Mario Bros. 3.
10. The Elder Scrolls III: Morrowind
9. System Shock
8. Gothic 2
7. Super Mario RPG: Legend of the Seven Stars
6. Metal Gear Solid III
5. Fallout
4. Mega Man X
3. Fallout 2
2. Super Mario World
1. Deus Flippin' Ex

Here's my top 10, based on how much they sucked me in on the first playthrough, and how much I loved them at the time. Keep in mind this isn't a critical assessment, but a "fun factor" list. I'll try to order them, but the order varies by mood.
1. Metroid Prime (amazing. So many "wow that was cool" moments)
2. Ultima Underworld (my first 3D game. An ergonomic disaster by today's standards - moving required holding down a mouse button. But a great game.)
3. Tempest (still my favorite classic arcade game)
4. Prince of Persia: Sands of Time
5. Duke Nukem 3D (awesome lan parties back in the day. Technically serial cable parties, but same thing really)
6. Jade Empire SE
7. Elvira and the Party Monsters (my favorite pinball machine. Is pinball allowed on this list?)
8. Legend of Zelda (not sure which one. The original was amazing at the time, Ocarina of Time added a lot to all genres, Link to the past was a great story.)
9. Star Wars KOTOR
10. Skies of Arcadia
I'm probably forgetting one, and will have to edit this later.
EDIT: OK, honorable mentions, stuff barely out of the top 10: Descent, Super Mario 3, No One Lives Forever, Ms. Pac Man, Soul Calibur (the original on Dreamcast), Sonic Adventure (also the original on Dreamcast), Grand Theft Auto Vice City (took the sandbox concept of the prior GTA's and refined it. Great music too. Post Vice City GTA's lost the magic IMO.). My very first "favorite game" was Asteroids. It seems pointless and simple now though.
EDIT: I can't believe I forgot Beyond Good and Evil. I think it should be at Number 4, as it ranks equal to POP:SOT. But then I'd have 11 games on my list...

Outcast (PC)
HoMM3 (PC)
Planescape : Torment (PC)
Might and Magic 6 (PC)
Dungeon Siege 1 (PC)
Androids (MO5)
Phantasy Star 3 (sega megadrive-genesis)
Wonderboy 5 (sega megadrive-genesis)
Gargoyle s quest (gameboy)
Soulblazer (Snes)

No order to these.
Total Annihilation
Mega Lo Mania
Syndicate
Half Life
Stunt Car Racer
Lemmings
Diablo II
Dungeon Keeper
Operation Flashpoint
Homeworld

You know, you can move around using WASDZXC. Quite enjoyable to play then actually.
As for my list, I cannot decide at all. Too damn hard.

Why do I love lists so much?
Anyway....
No order of preference.
Syndicate
Hired Guns
Wizball
Tie Fighter
Grand Prix Legends
Pilot Wings
Resident Evil 2
Paradroid
Uridium
Golden Eye 64