Alien Breed
Raptor

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

Freelancer !
I know there is an official wishlist, but I also want to introduce this game here, also because many people don't know it.
There aren't that many space-simulations out there, so I think if you are a fan of the genre you should at least download the demo/trial version.
You like Space-simulations like Freespace, Elite, Darkstar One, SpaceForce? Then you will love Freelancer! Explore the open and giant universe, pirate other players, police and traders, follow the storyline, fight against NPCs and in massive PvP-Fights in Multiplayer, trade goods for your wealthiness and experience the dynamic reputation system with over 30 Factions !
Greed, morality, compassion, anger... whatever motivates you, the dynamic universe will respond. Take the first step. The universe is waiting.
In Freelancer you decide by your own. Do you want to be the hero of the police? Or do you want to chill out and relax while you are trading? Or do you want the bad boy who attacks the navy, police & trader organisations? It is your choice !!
Screenshots:
http://www.microsoft.com/games/freelancer/ss.aspx?ss=fl_ss_ss_005">http://www.microsoft.com/games/freelancer/ss.aspx?ss=fl_ss_ss_005
http://www.microsoft.com/games/freelancer/ss.aspx?ss=fl_ss_ss_010">http://www.microsoft.com/games/freelancer/ss.aspx?ss=fl_ss_ss_010
http://www.microsoft.com/games/freelancer/ss.aspx?ss=fl_ss_ch_004">http://www.microsoft.com/games/freelancer/ss.aspx?ss=fl_ss_ch_004
http://www.microsoft.com/games/freelancer/ss.aspx?ss=fl_ss_ss_006">http://www.microsoft.com/games/freelancer/ss.aspx?ss=fl_ss_ss_006
http://the-starport.net/images/rsgallery/original/cwevent3ub4.jpg
http://the-starport.net/images/rsgallery/original/screen21.jpg
http://the-starport.net/images/rsgallery/original/screen15.jpg
http://www.abload.de/image.php?img=5y2u-6wy7u.jpg
http://www.abload.de/thumb/5y2u-6wy7u.jpg
Hungry yet? DOWNLOAD THE TRIAL VERSION FOR FREE NOW !!
http://www.freelancer-reborn.de/freelancer_demo.exe
And there are also some reasons to play back FL again if you already did due to some new developemented features & mods (I will write later more about this)
Also visit this page if you want to start into the Multiplayer:
http://www.freelancerpatch.com
Community Links:
http://www.the-starport.net (International Community site)
http://www.microsoft.com/games/freelancer (Official Site)
It is a great game and I believe many will agree with me here, it should be aviable at gog.com :)