Calling in my vote for the usuals:
+++++Mechwarrior 2: The Clans
+++++Mechwarrior 2: Mercenaries
Mechwarrior 2: Ghostbears Legacy
Mechwarrior 3
Mechwarrior 4 + Expansions
Mechcommander
Systemshock 1
+++++Systemshock 2
Homeworld 1
Homeworld 2
Final Fantasy VII
Deus EX
Tie Fighter
X-Wing Alliance
Jedi Knight: Dark Forces II
Sam & Max
Interstae 76'
Thief 1
Thief 2
Thief 3
Oddworld: Abe's Oddysee
Oddworld: Ade's Exxodus
Myst Series
X-Com Series
Starcraft
Metal Gear Solid
Metal Gear Solid 2
Baldur's Gate Series

Commandos.
Man, this game rocked. I still remember how hard it was. Make it happen, GOG.

Mind Rover: The Europa Project
Published by: CongiToy
Great game where you had to build little remote control cars and such to race and battle other units. This was definitely a thinking game as you had to wire your cars to run in a way you wanted them to run.
This game had a large following and I still have the guide they sold for it but no longer have the game.
I do no think you can buy it any longer.

Dungeon Keeper 1 + 2
Aquanox 1+ 2
Wheel of Time
System Shock 1+ 2
Rogue Squadron
Another World
Outcast
Final Fantasy Series
Lands of Lore Series
Nox

Old Sierra game called: Lighthouse. Well, I think that was the name anyway.

Black and White 1&2.
Wing commander (all)
Privateer 1&2

I'd love to see the Carmageddon games, plus any Splat Packs that came with it. I loved those games. I still own the original, but can't get it to run anymore.
I'd also love to see the Leisure Suit Larry games return, specifically the talky versions of six and seven.
Oh, and Transport Tycoon Deluxe... not to mention the other great strategy games like those.

Deus Ex
System Shock 2
Grim Fandango
Planescape
Temple of Elemental Evil
Arcanum (still have my copy but others need the chance to play it)
Witchaven 1 & 2

X-File: The Game - 1997
Blade Runner - EA / Westwood

man i would love some Carmageddon 2 : Carpocalypse Now (SCi / Interplay)
i had so much fun playing that game.
also it would be fun to see Neverhood again that was a cool game

Outlaws, Duke Nukem 3D, Starlancer, Freelancer.

Lands of Lore
Ishar I, II & III
Robinson's Requiem

Battlezone 1&2 (would be great if there was a way to get multiplayer to work through the site as well)
Baldurs gate
icewind dale