Speaking from personal experience, FF7 and 8 aren't that great on PC. If GOG could fix those issues, I'd be okay.
I'm waiting for id stuff (and not price gouged like on Steam, yeesh) as well as Deus Ex.
EDIT: And Morrowind.

Shadow Warrior, Dungeon Keeper 1 & 2, Age of Empires 1 & 2, Majesty + its expansion. Oh, and Heroes of Might and Magic II.

Jane's USAF

Shadow Caster ... Origin's forgotten gem where you could change shape and use magic and all that!

Any of the Koei strategy series. Genghis Khan 1 and 2, Nobunaga's Ambition 1 and 2, L'Empereur, etc.
But it would be nice to get the best versions of these not necessarily just the pc versions. I played these originally on the NES and in some cases those were better than the DOS versions.

I-War
Outcast
Homeworld
O.D.T.
Dune 2
Black Dahlia
Blade Runner
Theese are few of my wishes :-).

Wasnt ShadowCaster made by Raven Software, of Heretic/Hexen fame?
Corridor 7: Alien Invasion, by Intracorp.
Strife by Rogue.
Dark Seed, by I dont know who. :P

Shadow Caster was developed by Raven Software and published by Origin Systems. Chances of seeing it on GOG?? Slim to none, I'm afraid.

the first 2 soldier of fortune games would be awesome
just bought kingpin and blowing someone's leg off in that with the shotgun made me want to play SoF

1. Toonstruck - a great and twisted little adventure game that runs great with DOSBox. I have no idea who owns the rights at this point, though...
2. The Longest Journey / Dreamfall - I don't think Funcom would mind that extra bit of cash...
3. Lost Vikings / Lost Vikings 2 - Blizzard seems to have a "if we can't do it - noone else will" approach to online distribution. While it works great for SC, D, WC, and WOW (no DRM, only elaborate CD-Keys), there's no Lost Vikings available on their site... Although - it would seem that they only did the SNES version of LV2, while Interplay was responsible for the PC one :>. And we DO have the Interplay catalogue on GOG...
4. Monkey Island: Special Edition - releasing something like that on Steam and not on GOG feels like a slap in the face... I'd get it from D2D (if it was DRMless, of course) but guess what - it's region-restricted ><'...
I know it's, in a way, a "new" game... Then again - they're selling it for *$9.95*. Why not sell it on GOG for 9.99 and rejoice over the additional $0.04 profit ?
5. Planespace: Torment / Baldur's Gate - a bit ironic but I'd rather play them in English (than play the fully translated version of BG, rumored to be the reason CD Projekt didn't go under). Also - 6 CDs for one game are an overkill ;).
6. The Neverhood, XCOM, HoMaM 2 and numerous others...

Hexplore, isometric old-school RPG with voxel based graphics. You can rotate the camera 360 degrees yet it still looks like a 2D sprite based game! :D The game crashes when you run it on a fast modern processor and the game's hard to find, so it would be cool if GOG made a new, cheap version :)

System shock 1 and 2 and total annihilation.

It would be awesome if GoG brings Blizzard's classic games, The Lost Vikings and Blackthorne.

rollcage and powerslide. incredibly fun arcade racers.