1: Duke Nukem 3D
2: Fallout 2
3: Jagged Alliance 2 with 1.13 (Fucking Epic)

1. System Shock
1. Morrowind
1. Fallout
Yeah. They all deserve first place :D I love those games, killed so much of my lifetime playing them instead of getting life... Well, maybe I have more life now, but... Noone will ever give me that kind of experience again :'(

1.Hostile Waters:Antaeus Rising
2. Duke Nukem 3D
3. Unreal

Really hard to choose... But If I had to, I'd take this three:
1. Legend of Zelda - Ocarina of time. Unfortunately, my N64 is busted, but I recently played the "Master Quest" version on PC. What a great game. And the graphics are some of the best I've ever seen in a video game, much better than all those "high definition" games like Crysis.
2. Medieval II: Total War. Maybe the best strategy game ever, in my opinion - followed closely by Civilization IV.
3. Gothic 1. A role-playing game from Germany, I think it isn't very popular in other countries. Great atmosphere, interesting story, and a really cool hero.

1. Baldur's gate 2
2. Kotor 1
3. Neverwinter Nights 2 + Mask of the Betrayer

Favorites... hm
1. Final Fantasy tactics (coupled with the psp remake)
2. Fallout 2
3. Fire Emblem: Blazing Sword

1 Silent hill
2 Thief
3 System Shock
I love Silent Hill.SH is my religion. :)
And Thief and System Shock is a masterpiece.

Mikee, you played BG without the XP cap, aren't you? ;-)
so did i, 5 levels were not enough to properly kick sarevok's butt, imho)

Suikoden 2
KKND
Original War

Actually, I would kill for XP/Vista-compatible versions of SEAL Team and Wasteland. I mean, literally. So, GOG, if you need anyone, you know, taken care of. Just sayin'.
(The Operational Art is already XP-compatible. I keep copies of TOAW on my tablet notebook... oh, so good.)

Hem... hem...
1. Silent Hill 2 - I just love the Silent Hill series. I still have the creeps when I'm thinking about the path of madness of James Sunderland. It is also the sadest game that I ever played. And the music of Akira Yamaoka... dark ambient is just great!
2. Fallout - Atmosphere of the postnuclear world is amazing. And the story given on the Holodisks... Brilliant game!
3. Planescape: Torment - It's somehow different from the other D&D games. Maybe because it has a deeper storyline, more interesting members of the player's team (Ignus, Morte, Anna...). I don't know :P Anyway it is extremely good game!
There are many more but these are the games with the BEST plot ever! (IMO of course :P)

1 Heroes of Might and Magic
2 Civilization
3 Heretic

1) Doom II- This was my first game and I love it to death. I have played this game nearly everyday for the last 12 years. I have no intention of stopping either.
2) Heretic- My second game and love the fantasy twist on Doom. Fantasy is my favorite setting so this is be great for me. Don't play it nearly as much as Doom II but it has never left my computer except for a little downtime when it wouldn't work on Vista.
3)Duke Nukem 3d- I remember getting this game and thought it was the best looking game I had ever seen. I don't know what 3d realms did but the game was so unique with it's level design and one liners (who doesn't love those?). Many sleepless nights over this little gem here.
I am a big fan of shooters ;). Can never get enough of the old ones.

I love the whole concept of this site - and now realise from my emotions that I am more a retro PC gaming fan than a modern PC gaming fan! I can remember 15 years ago when I was buying 10-12 new, just released PC games a year. Now I buy 1 or 2, because the quality and gameplay just isn't there in most titles! I will not pay $50 for a game with 12-15 hours of shallow gameplay. They are the one's that should be selling for $5.99 and I wait until I can buy them at that price on ebay or bargain bins! Games with gameplay in spades, like STALKER and The Witcher I still buy, but it's getting rarer and rarer for me to buy new games.
I give you an example, I dragged out one of my compilation packs, bought for £9.99 ($17) around a decade ago. The compilation is called 'Ultimate Strategy' and these are the games that come in it:
Sid Meier's Civilization
Sid Meier's Railroad Tycoon Deluxe
X-Com UFO Defence
Heroes of Might and Magic
Conquest of the New World Deluxe
Jagged Alliance Deadly Games
M.A.X. Mechanized Assault & Exploration
Dark Colony
You could hardly have a compilation of about 3 games from the last 3-4 years that would match any of the above! Imagine the excitement back then of buying compilations and games with titles like this! That expectation just isn't there any more, as PC gaming has gone mostly 'corporate' !
This is why you gotta love G.O.G. and what they are trying to do - God Speed to them I say! May all our top 3's become famous again through G.O.G.! :)