I'm going to basically prove that SEGA wiped the floor with all other developers and publishers in terms of quality software throughout the 6th generation and anyone can counter this if they wish or submit to the might of the 6th generation SEGA lineup. Hopefully my Dreamcast infected cultists will back me up with this. From the beginnings of the Dreamcast to the ends of the PS2 lifespan, SEGA pulled out masterpieces. Genre by genre there was quality software which gave them an edge all around the board. There is no other developer or publisher that did more for gaming in the 6th gen. You're of course willing to argue this, but I don't see the point. Here goes:

Fighting: Fighting Vipers 2, Giant Gram All Japan Pro Wrestling 1-3(JPN), Godzilla Generations(JPN), Virtua Fighter 3tb, Virtua Fighter 4 Evolution, The Rumble Fish(JPN)

 Rail-Shooting: Panzer Dragoon Orta, Godzilla Generations Maximum Impact, Gunvalkyrie, REZ

 Racing: Crazy Taxi 1-3, 18 Wheeler American Pro Trucker, Daytona USA, Flag to Flag, Metropolis Street Racer, Sega GT,  Sega Rally 2, Toy Racer(EU), Sonic Riders, Ferrari F355 Challenge, Initial D: Special Stage(JPN), Outrun 2006: Coast to Coast, SEGA Rally 2006(JPN), Sonic Riders: Zero Gravity, The King of Route 66

Sports: NFL 2K-2K5, NBA 2K-2K5, NHL 2K-2K5, World Series Baseball 2K1-2K5, Worldwide Soccer 2000(EU), Virtua Athlete 2K, Virtua Striker 2, Virtua Tennis, Tennis 2K2, SEGA Marine Fishing, SEGA Bass Fishing 1-2, Rippin Riders Snowboarding, Net Golf(JPN), NCAA College Football 2K2-2K5, Beach Spikers, Home Run King, NCAA College Basketball 2K3-2K5, SEGA Soccer Slam, Virtua Striker 2002, SEGA Superstars Tennis

Action: Alien Front Online, Bomberman Online, Dynamite Cop, Ecco the Dolphin: Defender of the Future, Jet Grind Radio, Jet Set Radio Future, Ooga Booga, Outtrigger, Toy Commander, Zombie Revenge, Billy Hatcher and the Giant Egg, Shadow the Hedgehog, Sonic Heroes, Spartan: Total Warrior, Super Monkey Ball 1-2, Super Monkey Ball Adventure, Appleseed EX(JPN), Astro Boy, Gungrave, Headhunter, Headhunter: Redemption, Nights into Dreams(JPN), Nightshade, Shinobi, Tenchu: Fatal Shadows, Super Monkey Ball Deluxe, Virtua-On Marz, Otogi 1-2, Spikeout: Battle Street

Action-Adventure: Sonic Adventure 1-2, Shenmue 1-2, D2, Floigan Brothers, Napple Tale(JPN), Rent a Hero No.1, Sakura Wars 1-4(JPN), Blood Will Tell, Yakuza 1-2, Toe Jam & Earl III: Mission to Earth

Light-Gun Shooters: House of the Dead 2-3, Virtua Cop 2-3, The Typing of the Dead 

Vertical/Side-Scrolling 2D Shooters: Chaos Field

Simulation: Seaman 1-2, Christmas Seaman(JPN), Dream Studio(JPN),SEGA Gaga(JPN), Amazing Island

Puzzle: Chu Chu Rocket, Puyo Pop Fever, SEGA Swirl, SEGA Tetris, Puyo Pop Fever 2(JPN)

Compilation: Smash Pack, Sonic Mega Collection, Sonic Gems Collection, SEGA Genesis Collection, SEGA Classics Collection, SEGA Superstars

Strategy: Hundred Swords(JPN), Worms 3D, Worms Forts Under Seige

FPS: Maken X, Quake III Arena

RPG: Phantasy Star Online 1-3, Skies of Arcadia, Time Stalkers, Virtua Quest, Phantasy Star Universe, Shining Force EXA, Shining Force Neo, Shining Tears, Shining Wind(JPN)

Rhythm: Samba De Amigo 1, Samba De Amigo Ver. 2000, Space Channel 5

Minigame: Sonic Shuffle

Flight: Aero-Elite: Combat Academy

That's a pretty lenient bar you have for games to qualify as "masterpieces".

I have to agree...I thought you were going to list a game for each genre and then tell me about how they were masterpieces, but instead you simply listed every single game they made. To which I say..."meh"

sega? are u kidding me? who bought those games?

for me it was EA, bungie, rockstar, insomniac, man others im to lazy to think of.

but sega? noooooooooohhhhh not sega

In Bold are the games that are either masterpieces or that somehow changed gaming. I've included the other because you did include a lot of mediocre titles too.

Fighting: Super Smash Bros. Melee

Racing: F-Zero GX, Mario Kart: DD, Kirby Air Ride, Wave Race: Blue Storm

Action-Adventure: Super Mario Sunshine, Luigi's Mansion, Legend of Zelda: Wind Waker, Legend of Zelda: Twilight Princess, Mario Vs. Donkey Kong, Pikmin, Pikmin 2, Metroid Fusion

RPG: Pokemon R/S/E, Pokemon Colosseum, Pokemon Colosseum XD: GoD, Paper Mario: TTYD, Mario and Luigi: Superstar Saga, Fire Emblem, Fire Emblem: PoR

FPS: Metroid Prime, Metroid Prime 2: Echoes

Strategy: Batallion Wars

Simulation: Animal Crossing


Sports: Mario Golf: TT, Mario Power Tennis, Mario Strikers

Rhythm: Donkey Konga
Party/Minigame: Mario Party 4, Mario Party 5, Mario Party 6,
WarioWare, Inc.: Mega Microgame$!
WarioWare, Inc.: Mega Party Game$

--

So, Nintendo had matched quantity and I believe superior quality to Sega.

I'd say Nintendo. Think about it. They have at most two platforms to sell their games on and they are at lowest the #2 developer according sales, just behind EA who makes games for every possible platform there is.

Eh... Who cares? Those are just sales.

I would have to say Nintendo, and then I would go with Capcom for 2nd place. 

 Just sales? Obviously good, quality games have some relation to high sales MOST of the time.

^all in favor say eye

Superchunk

For some reason, Nintendo's best games aren't the best selling. Their not as good games tend to sell better.

And to show something, even though I dislike using GR, that is the only way I can give some facts, and even a little biased facts are better than no facts.

Top Sega games last gen:

On GC:

NFL 2K3 = 22nd place, 89.6%
Super Monkey Ball = 30th place, 88.6%
SM Ball2 = 52nd place, 85.2%

On Ps2

VF4: Evolution = 23rd place = 91.4%
VF4: = 35th place = 91.1%
NBA 2k2 = 54th place= 89.6%
Then 13 titles in 85-90%

On XB

Panzer Dragon OoRta = 18th place = 90.4%
Then 9 titles in 85-90%

So overall, Sega had 29 titles in 85% + last gen. Not bad, but you should have said "3rd party developer", then it would have been more reasonable.

Capcom:
Best on XB = 122nd place, none in 85% +
Best on Ps2: = 1st place - RE4. Also 14th - Okami. 6 titles in 85% +
Best on GC = 2nd place - RE4. Also Wietifull Joe at 8th, and RE at 12th. Total games in 85% + = 4

So Capcom has the 2nd and 3rd best game in the entire generation, and 8 other titles of 85% +. Capcom has a bit better quality than Sega, but not as many good titles.


Electronic arts:

ON GC = 21 titles in 85% +. Best at 5th place, and then 10th and 13th, 14th and 15th.

On XB = best, 7th, 16th and 22nd. Total in 85% +: 26

On Ps2: best, 9th, 10th, 11th and 16th. total in 85% +: 33

So EA has almost as good top quality as Capcom, a bit better than SEGA, and has 80 titles with 85% +. I'd say it's not even a question. EA takes the spot. At least for consoles only.

Nintendo? Not a change. Only 15 titles with 85% +. (Although 6 at 90% +, so no other can beat them in quality alone)

On a side note, Nintendo has already made 3 90% titles on Wii, and 5 in 85% +.