Dungeon Keeper 1 & 2
Crusader No Remorse & No Regret

In addition to my previous list I'd like to add my support to Freedom Force (that was outstanding... never played the sequel though) with bonus content being the additional fighters that were available for preorders before...

As my profile pic would suggest: BALDUR'S GATE! all of 'em!
But also:
Planescape: Torment
Arcanum!
Albion
Darklands
Cave Story (GOG could always use more free games, but I'd be eager to pay money for it!)
All of the X-COM games
The Monkey Island series
The Serious Sam series
The early Total War games (Shogun, Medieval 1)

I'm going to vote for Desperados: Wanted Dead or Alive, as well as its two sequels. :)
The first game is a 2D Commandos-style point-and-click Western strategy game (though you can forgo strategy on many levels, and just shoot stuff), the other two are in 3D.
Hmm, while here, I might as well add Commandos to the wishlist. :D
Very tough 2D WWII strategy game, but it had a lot of style to it.

Shogo?

master of orion 2?

Just to keep this alive... and because I just ran into a game from my youth somewhere....
Dominus
http://www.mobygames.com/game/dominus
This was a fairly tricky but very rewarding game played in dos - well worth tracking down if you see it at a flea market, ebay etc... or if the GoG team can get in contact with the old devs/publishers for distribution rights.

Might and Magic series would be great.

Come on everybody, only above 200 wishes and Mafia 2 is its way.
Maybe the GOG team should contact the owners of the Mafia IP to help them grow the interest for Mafia 2.
lets vote for Mafia everyone!
http://www.gog.com/en/wishlist/

Holy carp! I fail at looking!
*goes to get Shogo*

I just gotta point out that the ONLY thing preventing me from buying Broken Sword II & III is the lack of Broken Sword I

Shogo!

GOG should consider Silent Storm gold from the Jowood catalogue as a surprise release.

System Shock 2, Daggerfall