I don't know. I know that Nintendo probably paid Capcom and Namco for their "exclusives", but it hasn't seemed to gotten Nintendo anywhere.
Of the so-called Capcom 5, this is what has happened so far. 1 (Dead Phoenix) got cancelled, 2 (Viewtiful Joe and Killer 7) are getting PS2 ports, and 2 (P.N. 03 and Resident Evil 4) are so far still exclusive to the Gamecube, with RE4 most likely to be ported eventually to PS2, no matter what Capcom is saying now.
As for Namco, I don't think Nintendo paid them per se, but they did give Namco some of their flagship franchises to develop, including Star Fox Armada, Donkey Konga, and even the Pikachu demo that was on the DS for E3.

In return, Namco makes Tales of Symphonia and Baten Kaitos for the Gamecube.
I think negative press is almost what's really hurting Nintendo. While I don't think Sony or MS would actually pay developers not to put games on the Gamecube, I could see the case for Sony or MS paying gaming press to hype XBOX and PS2 and diss the Gamecube. Play for example, was really excited about the DS when it was first announced, but "suddenly" after E3 they were giving it negative press and hyping the PSP. While they may have just changed their minds, I kind of found it strange.