Rockstar (GTAs/Manhunt) defined the new mature-geared games industry, and Konami as far as great fucking game development overall (Silent Hill 2-4, MGS, ZOE2, and more).
For myself, Nintendo and their gaggle of 2nd party development houses. Some can complain all they want about particular points, such as Mario Sunshine not topping Mario 64. But, ratio of quantity to quality? A "B" game from Nintendo (Sunshine, Wind Waker) eats most other developers' triple-A titles for breakfast and craps 'em out by lunch.
Add to this:
Intelligent Systems, the Guys That Can't Make a Bad Game.
Alpha Dream's insane work on GBA Mario RPGs
Retro performing a bonafide miracle from God and transforming one of the best 2D games of all time into a FIRST PERSON 3D game and not losing anything in the process.
Rockstar left the biggest footprints on this generation, obviously.
Nintendo is still doing what Nintendo has always done (EAD, Retro, Intelligent Systems), develop and publish superior software.
Ubisoft obviously produced some great games this gen (POP:SOT is their best, IMO).
Sony's first-party offerings made great strides this gen, thanks to ICO, God of War and Shadow of the The Colossus.
But my personal fave this gen was Capcom (and its subsidiaries like Clover): they introduced more worthwhile IPs than any other dev, and they did it with unmatched pinache: Viewtiful Joe is a retro-gaming masterpiece, gotta love the look of Okami, RE4 speaks for itself, Devil May Cry is the best new IP this gen and has become an elite action series; they also developed the incredible Minnish Cap. Love that Capcom!
Amusement Vision - Super Monkey Ball, Super Monkey Ball 2, F-Zero GX Intelligent Systems - Fire Emblem, Fire Emblem: Sacred Stones, Advance Wars, Advance Wars 2, Advance Wars DS, Paper Mario 2, Fire Emblem: Path of Radiance, Mario Kart Super Circuit
My personal votes would go with: 1. Intelligent Systems - Fire Emblem, Fire Emblem: Sacred Stones, Fire Emblem: Path of RadianceAdvance Wars, Advance Wars 2, Advance Wars DS, and Paper Mario 2, 2. Amusement Vision - Super Monkey Ball, Super Monkey Ball 2, Beach Spikers and F-Zero GX 3. Retro Metroid Prime 1 and 2 (2 wasn't THAT bad...whiny bitches)