Crusader: No Remorse, No Regret
System Shock 1, 2
Knights of the Sky
Sam and Max: Hit the Road
Commandos 1, 2
Earthworm Jim 1, 2
EDIT:
Thief 1, 2

I second this :)

Crusader: No Remorse and No Regret
Little Big Adventure 1-2
Messiah (some may have it working on windows xp but for me it has never worked)
M.A.X and M.A.X2 (mechanized assault and 'xploration')

The old adventure games, like the Monkey Island, Simon the Sorcerer and Indiana Jones series.
More old stuff in general, like the Commander Keen & Jill of the Jungle games.
Fury3 and/or Terminal Velocity
+1 Might and Magic.
Lemmings ^^
The old Elder Scrolls games (I'm sure they were mentioned already, just adding my vote).
The Ultima games would be sweet, although I think the Underworlds had some kind of licensing issues?
That's all off the top of my head....
EDIT: +1 Dungeon Keeper, and also The Incredible Machine games
EDIT2: +1 to The Settlers series! (mainly #2 for me)

Uprising: Join or die
Sub culture
Screamer
I already own the above games but it would be good for others to experience them. :)
I had Mechwarrior 2 but did not really play on it much and lost it. Would be great to have another chance to play.

Clive Barker's Undying
Duke Nukem 3D
Sanitarium
Any of the Baldur's Gate Series

I'd love to see:
Alpha Centauri
Planescape: Torment
Baldur's Gate Series (I actually own an original copy of the second and it's expansion, but can't find the first one anywhere...)
System Shock 1 and 2. (PLEASE...)
X-COM UFO Defense

Lighthouse was a fun adventure game I would like to see it on there

Anyone else remember... Die by the Sword?
That game rocked.

anyone remember the Myth series?
Myth and Myth II: Soulblighter
Originally made by bungie, eventually Mumbo Jumbo made Myth III: The Wolf Age or something.
I'm mainly concerned about getting Myth 1 and 2 :D

It would be great if these were avaliable:
Constructor (and Street Wars)
System Shock 1 & 2
Planescape Torment
Warhammer SotHR & DO
Theme park world
Theme hospital
Emeror: Battle for Dune (or Dune 2000)
Homeworld series
Might & Magic series

My god, I should have thought for a longer second!
Die By The Sword
Theme Hospital
Gangsters

Games I would love to see on GOG:
System Shock 1 & 2
Deus Ex
Mechwarrior Series
X-Wing and Tie Fighter
Thief
Elder Scrolls Series (not Morrowind or Oblivion)
Arcanum
Might & Magic Series
Bard's Tale Series
Any game with Quest as the second name in the title: King's Quest, Space Quest, etc
Adventure games

From Lucasarts:
Monkey Island series
Maniac Mansion 1 & Day Of The Tentacle
Full Throttle
Sam & Max Hit The Road
Indiana Jones and the Fate of Atlantis
From Sierra:
Space Quest series
Gabriel Knight series
Leisure Suit Larry series
Police Quest series
King's Quest series
Conquests of the Longbow: The Legend of Robin Hood
Straight from an adventure games fanatic :)

I haven't had time to read the entirety of the thread here, but I am hoping I am not the only one that has fond memories of:
Wing Comander: Privateer
Privateer 2
Strike Comander
Wing Commander: Prophecies
WIng Commander 4
Wing Commander: Kilrathi Saga