Might be a bit long, but these games I'd gladly pay for again as most no longer run in Vista and/or I no longer have the discs, etc, for them

Missionforce: Cyberstorm 1
Like mechs? Like turn based tactical strategy games with resource management with mechs AND their pilots? Like explosions? Like customizing your mechs from the ground up?
This game's for you. ;-) (But not 2, Sierra Sierra'd it.)

Full Throttle
No adventure game lover should miss this one. Great humor, great soundtrack, fluid animation, lots of attitude.

Syndicate
How could you not?

STRIFE
Such an underrated game. Yeah, they used the DOOM engine, but graphics ain't everything, am I right?

Privateer 2
You've got all the Wing Commanders except Prophecy, you've got Armada and the first game, time to round that collection out.

Shivers
Yes, the "demon" animations just about killed all the suspense and genuine creepiness that the atmosphere and story conveyed, but you gotta admit, this game probably made you jumpy after playing it at night with the lights off.

Crimsonlands
Great mindless shooter.

Starflight
This game was a far more serious version of Star Control and both games' influence can still be seen in games like the first Mass Effect to this day. Part rpg, part exploration and trading sim, part combat, it was a little bit of everything in a massive universe that made you keep a physical map on hand to remember where the alien races, etc, were.

Legacy of Kain: Blood Omen
Great game and one I played for many hours.

The Hardball series
Great series of baseball games and I could see there being a market for this, considering Accolade no longer exists AND due to the physical DRM in the form of codewheels, the abandonware option really doesn't exist here either, as you'd be dealing with cracked versions and the like. =\

Age of Empires Gold
Would LOVE to play this again without the Ebay/Amazon option.

Blade Runner
I'm missing ONE disc from the CD copy I bought. ONE. :(

Kohan: Immortal Sovereigns + expansion
I literally spent DAYS playing this game, getting my heroes and leaders up to max levels, messing around, playing multiplayer. Would love to see this game on here, considering Strategy First allowed Disciples. ;-)

STALKER: Shadow of Chernobyl + Clear Sky
Would also love to see this game here.

Warlords series
You've got Battlecry, Age of Wonders, HoMM, King's Bounty? Why not one of the originators of the genre?

I'm sure I'll think of more later, kick myself and come back to add to the thread. :3

I would love to see Ripley's Believe It or Not!: The Riddle of Master Lu. It was a great adventure game. :D

I want Metal Fatigue dammit!

command and conquer gold for win95 was released for free.

and tiberian sun as well.

System Shock 1 & 2

The Neverhood

Warhammer 40k: Chaos Gate, Final Liberation, and Rites of War

Mechwarrior 2 & 3

Outlaws

Still.. All Discworlds.

I have looked for these 2 games for years. It would kick butt too play them again!!

Privateer 2 for sure!!!!

Full Throttle!!!!

Aliens vs Predator 1 and 2

Theme Hospital

Doom I & II (Doom II is already abandonware)

Legacy of Kain: Blood Omen

Lucasarts adventure games(hardly possible, but would love to play Curse of Monkey Island and Loom sometime)

Age of Empires (Not really feasable as it is owned by Microsoft game Studios)

Rise of Nations Finally one that I would definitely pay for is Rise of Nations!!!!!!! This game is LITERALLY NOWHERE to be found nowadays.

Worms!!!!! (also Liero would be a good choice for 5,99)

Penumbra ( not that old... but it is definitely a GOOD GAME, besides, I'm pretty sure the GOG userbase would like this game)

Red Faction (ph yes...come on)

The Neverhood I know some people remember skullmonkeys, so why not?

GUBBLE: Finally... I would actually pay to play GUBBLE again...(yeah, I'm pretty sure I've made some fo you google that, but trust me, nostalgia overload will be worth it)

I'm not mentioning the games everybody has always mentioned (I'm looking at you System Shock), and I would love if some people agree with my choices.

Battlezone (1998). Fun hybrid of a tank simulation game, a first-person shooter and a real-time strategy game. The best part was how it all worked together quite well.

Warhammer 40k: Chaos Gate. A very good tactical squad game using the always fun Warhammer 40,000 IP.

I would LOVE to see Syndicate Wars on here (and also Syndicate). I bought Syndicate Wars years ago and never got around to completing it, but I think it was a fantastic game.

Also Theme Hospital.

Please! :D

Theme Hospital...that is pretty much the 'big' one I have wanted since I have been on the site (3 years and waiting) :P

Activision Battlezone I&II (Oh, please)

Syndicate

MechWarrior 2 & 3

MechCommander

I would love to see MechCommander 1&2 on gog.

Personally, I would love it if GOG struck up a deal with Falcom to release localized versions of the Ys series. There is about 7 or 8 different PC games from that series, and it shouldn't be hard to arrange for localization if GOG can permission from unofficial translators to use their work. It would also be nifty if Capcom could release their Phoenix Wright games via GOG, too.

EDIT: Oh, and to release versions of Snatcher and Policenauts. Both of these games were made by Hideo Kojima, the guy who made the MGS series. I would argue that these are actually superior to his MGS work, largely because they are self-contained stories.