This is a tough call, but ultimately I have to go with Banjo Kazooie. It took the formula established by Mario 64 and elevated it to a whole new level. From its brilliantly designed worlds, to its sense of humour, to its soundtrack, its the best game of the 5th generation in my book.

Donkey Kong Country 2 is a very close second though, and similarly wins my pick for best game of the 4th generation. 

Rare was just too good in those years. I still maintain that Rare 1994-2001 is the most accomplished run by a single developer, ever. The studio pushed the limits of Nintendo hardware, experimented with different genres, and produced some legendary games in the process.

Banjo Kazooie. A great collectathon platformer that, unlike DK64 or Tooie, didn't go completely batshit crazy with the colletables.

Conkers then Perfect Dark. I loved being able to sick the AI teammates on specific players or tell them to protect me, defend the hill, ect.

I have to agree, I can't think of any other single developer that achieved so much within such a timespan.

There are others (though VERY few) who have reached a similar level of quality, but none who have simultaneously been so prolific. 

Conker because it's one of the most charming games I've ever played. Banjo Kazooie and DKC2 are also pretty damn good.

PD with BK on 2nd place and DKC2 on 3rd.