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I'm going to have to go with Nintendo on that one.  Mainly because of the Zeldas (OoT and MM), Mario 64, the first Smash Brothers, Paper Mario, Star Fox 64, Pokemon Snap

 

Rare was awesome though putting out some timeless games.  If I had to do a scale from 1 to 10 on their output, Nintendo would be at an 8.5 in quality games that gen, with Rare at a very close 8.1-8.3 for the Banjo games, Diddy Kong Racing, Donkey Kong 64, Conker's BFD, Jet Force Gemini, Perfect Dark, and Goldeneye.