Rare's partnership with Nintendo is by far the most successful in the history of the industry. Other successes include Retro, Naughty Dog, and Bungie.
I'd rank them in this order;
1) Rare/Nintendo (1994-2001)
2) Retro/Nintendo (2002-present)
3) Bungie/Microsoft (2000-2007)
4) Naughty Dog/Sony (2001-present)