Bungie

Insomniac

Nintendo (Zelda team) aka EAD Software Group 3

Nintendo
Konami
Capcom

EAD Software Group Tokyo
(Responsible for titles such as Super Mario Galaxy and Donkey Kong Jungle Beat)

EAD Software Group 3
(Responsible for titles such as Ocarina of Time and Wind Waker)

Retro Studios
(Responsible for the Metroid Prime series)

Class Acts all around.

*If you would have asked this question 15 years ago Sonic Team would definitely be up there. Oh how times have changed.

Insomniac
Valve
Bungie

#1: Nintendo (I have to pick one? Uggghhh... Zelda team then);
#2: Konami/Treasure;
#3: Capcom;

Nintendo EAD Group 3 led by Eiji Anouma - Legend of Zelda
Team ICO - Ico, Shadow of the Colossus
Kojima Productions - Metal Gear Solid 1-4

Three favorite current studios:
SCE - God of War, Syphon Filter, Loco Roco, Patapon
Level 5 - Dark Cloud, Dragon Quest 8, Jeanne d'Arc, Professor Layton
Ready at Dawn - Daxter, God of War: Chains of Olympus

Three favorite developers of all time:
Sega - Phantasy Star, Toejam and Earl, Skies of Arcadia, Panzer Dragoon Saga, Virtua Fighter, Crush
SCE - God of War, Shadow of the Colossus, Syphon Filter, Patapon
Konami - Castlevania, Contra, Metal Gear, Silent Hill

1. Konami (Suikoden, Winning Eleven, Metal Gear, Silent Hill)
2. Sony Computer Entertainment (ICO, Shadow of the Colossus, God of War, Gran Turismo)
3. Atlus (SMT, Persona, Tactics Ogre)

1. Nintendo
2. Blizzard
3. Square-Enix

 No love for Ensemble? Oh wait..

Treasure, and Blizzard are my two favorite studios. No other studio has made games well enough with any consistency to be worth mentioning in the same breath as those two.