There have been a few development studios under Midway (including several Midway Studios) that have made some of my favorite games of all time - NHL Hitz, NBA Jam/Hangtime, etc. Seeing that publisher go under made me sad.
I'd also like to list Capcom Studios 4, and SCE Japan. And of course Nintendo has had their own in-house development teams from the beginning, all of which I'm a big fan of.
As for current indie teams, ThatGameCompany, Playdead, and The Fullbright Company have my full attention!