The Delta Force series (I'm partial to Black Hawk Down), if Steam can do it, GOG can do it better!

Worms Armageddon and/or World Party!!!
I would die for Armageddon with full support for Vista

Is this the Worms game I'm thinking of, a turn-based game where you shoot worms in a side-scroll view for no reason?

Yup, both Armageddon and World Party are basicly the same.
Just that Armageddon still has a lot of users playing online, and World Party had more single-player content.
They were the last good 2D Worms

Crusader: No remorse, Crusader: No regreat!!!

I would like to try little big adventure.

Well, the obvious one first:
planescape torment
Then Outcast would be nice and the entire legacy of kain series :D

Yeah, I'd like to see some space quest...

I for one have often tried to make Fantasy Empires from TSR work on my older machines. None of my junkers can even run it tolerably. I own the game and would gladly pay for a version that works on current generation systems. Last time it ran well was on a 66mhz machine I've long since lost.
This was easily the first game to perfectly combine turn based and real time strategy with a bit of RPG and even MMO type persistence. Of course many games like Dark Legions followed but the original FE was the BOMB. Hot seat fun for days on end. Find a way to make this work, maybe even make a TSR bundle with some of the other games that came out in the 90's like this.
The other title I would love to see working on current machines better is Axis and Allies. But I'm sure Hasbro has plans for more current versions of that.

You know, my past is as a console gamer, so I'm going to... bend the "PC Only" rule a bit here. =P
I'd love to see Konami's Collector's Series: Castlevania & Contra, Sega Smash Pack Vol. 1 & 2, Sega Puzzle Pack, Taito Legends, Virtua Fighter 1 & 2, Atari: 80 Games in 1, Activision Anthology, Metal Gear Solid Integral, Tomb Raider 1-3, and Final Fantasy VII & VIII.
Hey, they are all PC Games... I'm just bending the rule like Earthworm Jim does!
But in terms of REAL PC stuff, I'd love to see the id Software catalog and the SimCity games on GoG.

Hey don't worry, i would happily see the rules bent for Final Fantasy VII and VIII and since Square-Enix have recently released The Last Remnant and Yosumin on PC perhaps they may becoming a little more PC friendly, fingers crossed.
Tomb Raider is a pain to get to run on a modern OS as well so even though I own it I wouldn't be against buying a GOGified version of that either or most of the others either:)
To the wishlist!

Faces of War.
If emulated Playstation games are ever allowed:
Any of the Front Mission series.

Wing Commander and Wing Commander 2, Strike Commander, Gunship 2000, Populous, Power Monger, Might & Magic III and Might & Magic World of Xeen. Spent a lot of time playing these games.

i have never experienced the wing commander series

I really enjoyed playing the Wing Commander series. I still remember installing them on my 386. All those 3.5" floppies! I can't tell you how many hours I spent playing them.