I love Bioware, games like Mass Effect and Knights of the old Republic were very memorable and so was MDK 2, which doesn't get brought up when people talk about Bioware these days. Ubisoft also, if for no other reason than that they gave me two masterpieces from Michel Ancel(Beyond Good and Evil and Peter Jackson's King Kong). Prince of Persia: Sands of Time was pretty sweet too. I like Squaresoft for the Final Fantasy games(and other interesting stuff like Einhander), though the company pisses me off sometimes. And of course Rare for giving me Battletoads, Viva Pinata and Conker's Bad Fur Day.
The only other companies that pop into my head are not exactly third party companies(Sucker Punch, Team Ico and Sega)
I'm surprised no one mentioned Treasure yet
EDIT:Oh I guess someone did mention Treasure