I would have to go with Bullfrog Studios here

Planet Moon. Wait, never mind, they were here all along :)
I'd most like to see Looking Glass.

Paragon Software
New World Computing
Origin
Microplay
Microprose

I'd love to see the SSI catalogue start to show up. The gold box D&D games, 5 Star General series, Wargame Construction Set series, Steel Panthers series, etc., etc., etc. I'll also second Qikdraw's mention of Microprose.

Yes I too would love to see the old SSI games particularly the gold box D&D games, I think they would have to go threw Ubisoft, as Ubi has the rights to SSI IP, and maybe Atari since Atari has the right to D&D cRPG games.

Aye. Failing that, would you settle for Eidos?
I'd also love to see LucasArts (SCUMM FTW!), Team 17, Microprose, and Westwood (too bad EA ate them :().

I'm torn between Bullfrog Productions and Looking Glass Studios. Origin's presence also wouldn't hurt.
If New World Computing's catalogue was added to GOG, that would be the perfect opportunity to refamiliarize myself with a subset of old Might & Magic titles that had "* of Xeen" subtitles IIRC. It's been ten years or so since I last played or even seen them.
MicroProse's support would bring X-Com and a ton of classic flight sims. GOG could possibly even start selling the classic Falcon 4.0 (NOT Allied Force!) for those who want to take the Open Falcon or Red Viper routes.

Sir-Tech, SSI, Microprose - these are the names that come to mind when thinking of companies responsible for styles of gaming that had faded into the past in recent years. And for no good reason: there are plenty of real gems there, for sure.
I'd also add a personal favourite: Blue Byte. I really liked the original Settlers and Incubation.

I think Atari owns Microprose IP as well, as SSI IP.

3D realms, i wanna play some good ol' duke nukem.

LucasArts and MicroProse, but both are pipe dreams.
LucasArts holds such tight control over all their IPs that no one will ever get them, let alone a site that would like to sell them without DRM.
MicroProse has been so broken up over the years that most of their IPs are spread over multiple publishers. Atari used to own all of what was MicroProse (MicroProse was bought by Hasbro Interactive, who was bought by Infogrames, who changed their name to Atari), but they have been selling off parts of it piece by piece over the years. For example, they sold the X-Com IP to 2K Games back in 2005, which led to all of the old X-Com titles being re-released on Steam a few months ago. Who knows where the rest of MicroProse's former IPs are these days.

Yes, if we're talking publishers then Eidos would be somewhere at the top of my list. Deus Ex, Thief and Legacy of Kain would be major attractions.
EA would be a particularly tough nut to crack, but I'd love to see System Shock, Ultima Underworld, Syndicate, Wing Commander, Crusader and Strike Commander here.

Legacy Interactive
[I am hunting for their Emergency Room series and can not find a way to purchase it]
Valusoft
[Love their 18 Wheels of Steel series, probably will love other games]
Team17
[Worms and...hmmm...Worms?]
Electronic Arts
[Why not?]
Sierra
[Some sweet classics. Quest for Glory, Caesar, Hoyle Casino, King's Quest, 3-D Ultra Lionel Train Town Deluxe, and many more... Yummy]

Looking Glass (for obvious reasons, but one can always dream)
Sillicon Knights (For Blood Omen Legacy of Kain, the only one in the series I didn't played)
Infogrames (today, they're with Atari. They made so many awesome games).
Origins
Eidos (for some old titles like the old Tomb Raiders).
These are on my wishlist