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I didn't play the Banjo games or Conker's Bad Fur Day, so it's not a fair comparison. But Ocarina of time > everything else for me. Mario 64 > Donkey Kong 64. Goldeneye and Perfect Dark (especially the multiplayer) were awesome and I would probably prefer Diddy Kong Racing above Mario Kart. But I would say Star Fox and F-Zero were fantastic as well (Wave Race was really nice, but didn't have the same replayability).

So the amount of great games. I would have to say: Nintendo > Rare.

For Best Game: Nintendo > Rare.

If I would have played the Banjo games. I could have said. Top 4 games for both: Rare > Nintendo.

But I didn't. So Nintendo wins ;)