To quiet that base fan, run it off 5V or 7V. You get 7V between the 12V and 5V lines on the disk drive power connectors, and that's a good voltage to run a fan slowly enough that it's quieter than the HD, but fast enough to keep the cube cool. 55°C is warmish for the GF6200, but if it doesn't get hotter than that when running the Flurry screen saver or other GPU-intensive work, it's OK. Mine wants a little fan of its own. That makes a nice setup for a cube. Mine is similar to yours with a 1GHz Sonnet G4 added, and I built a subwoofer to match.

http://www.cubeowner.com/forums/index.php?showtopic=13516