Nintendo, no contest. In fact, Nintendo should be automatically disqualified for being too godly.

So, considering Nintendo is disqualified, I'll go with Kojima Productions and Nippon Ichi for the tie. I'm not a huge Metal Gear fan, but there's no denying the quality of those games. However, Zone of the Enders is one of my favourite game series. If that was on the PS3 at launch, I would snap it right up.
Nippon Ichi's games have a real charming quality to them that surprised me. I like companies that do things differently.