Xbox:
Team Ninja - These guys aren't human. They remind me of old Genesis teams that would sweat every line of code and optimize for six months straight, like Treasure. Ninja Gaiden is amazing, but I still can't believe I'm seeing DoAU with my own eyes.
Sega - The Panzer Dragon Orta team really knows their sh!t. Nuff said.
Bizarre - The Project Gotham games are a great balance of beauty and power. PGR2 still has some of the nicest stuff on the Xbox.
Gamecube:
Capcom - A lot of their teams really have come far in 3D graphics and show off Capcom's artistic ability to the maximum.
Sega - AV rules. F-Zero GX pushes my eyes to the back of my head while looking beautiful.
Nintendo - Say what you will, but this generation Nintendo began focusing on pushing the hardware more, though generally with one or two brilliant effects in each given game. Zelda - TWW however is flat out impressive however you slice it. Best cel shading engine so far bar none.
Retro - Metroid Prime series. Speaks for itself.
Playstation 2:
Sega - When Sega actually bothers to care, they still know how to grind the metal. AM2's Virtua Fighter 4 conversions are triple AAA productions considering the specific hardware weaknesses of PS2.
Polyphony - They take forever to make a game, but jesus christ. Just... christ.
Naughty Dog - Masters of the epic scope 3D gameplay engine. Every game they make is among the elite of its year.
Square Enix - While they typically don't push the blistering frame-rates most gamers seem to equate with visual quality, they go craaaaazy with every visual trick possible on the hardware. No resource is left untapped - especially if it involves summoning spells
Namco - They're the Team Ninja of Playstation systems. You can count on them to deliver rock solid performance with great visuals and design, as well as character models.
Konami - Konami is like Square - igenuity and effects over raw performance such as framerate. MGS3 though, is definitely pushing the hardware to the edge.