Sega has made far more great games than I can count or keep track of. Konami would have gotten my vote on most other lists, but Sega has just made so much from all the great Genesis games (Sonic, Shining Force, Phantasy Star, Flicky), to great arcade games (Golden Axe, Altered Beast), to great modern games (Puyo Puyo Tetris, Valkyria Chronicles) etc.... So many great Sega games I can't even list them all.
Now I would probably rate Platinum games third. They are good, but the fact that they now have more votes than Sega shows how biased the voting is toward the recent batch of games. They just haven't been around that long.