I miss Legend Entertainment the most. Some of my favourite adventure games were made by Legend:
Eric the Unready
Spellcasting series
Gateways
Callahans saloon

Black Isle without a doubt.

Origin,Troika Games and Looking Glass Studios are probably the foremost ones.

At the risk of sounding cliche, gotta be Black Isle, Looking Glass, and LucasArts.
SSI and New World Computing, too. I also wish Troika had stuck around long enough to realize their full potential.

Some of my faves: origin, sierra, interplay, black isle.

That's a tough one.
I miss the old Interplay actually, the mid'ish 90's era Interplay that had studios like Black Isle and their logo "By gamers for gamers."
I also miss Bungie, the bungie before MS that was focused on developing pc games like the Myth series and even made their games for both pc and mac and one of the few companies that did with new games.
Then there's Origin, Westwood, and Bullfrog, all great studios that got swallowed by EA.

I definately miss the classic Sierra, INN was a fantastic idea shame it didn't work out though I've been playing on the revival server. They did so many things right with KQ and SQ and LSL not to mention Red Baron still is higher on my list than any WW Dogfighter since.
I also miss Black Isle though I guess I'm happy with DA:O coming out.
And finally I miss Westwood, they made some awesome games.
I would add New World Computing to the list, but I'm not so sure a classic Might and Magic style game would work these days.
I wish Microsoft would release quality Mech games for the PC again, I loved the MW and MechCommander series'

Sierra, for their pure adventure games. I did not like them bashing LucasArts though. :(
Soon Id Software now that they got bought out. :(
Infocom, for it's mighty and many text adventure games. Many fans still to this day boot up there computers just to see, "You are standing in an open field west of a white house, with a boarded front door. There is a small mailbox here." :(
Oh I forgot Keypunch Software, without those dinky puzzler games to figure out my life would of been boring. CTRL-O exits the game? :)

Black Isle without a doubt. That studio had so much awesomeness packed into it :(.

Origin Systems, Inc.

oops, forgot about westwood, one of the greats

id software. Now they are bethsoftware. : (

Papyrus for me.
I'd kill for another Grand Prix Legends.

Origin, Sierra, Black Isle, Troika, Westwood, Bullfrog...
So many names, good developers.
Fallen, but never forgotten.

LucasFilm Games.