Been looking for this WAY to long, so now I've found the solution, I'm preserving it here for posterity. Ohai, posterity.
I use a Apple USB keyboard (the small one, without the keypad. Who uses a keypad??) with Ubuntu 10.04 (Lucid). I've been wanting to switch the functions of the control and command keys for forever, but never found the solution.
It's remarkably simple. Open System -> Preferences -> Keyboard. In the 'Layout' tab choose 'USA Macintosh' as default layout. Then hit the 'Options' button, and under 'Alt/Win behavior' mark the option 'Control is mapped to Win keys (and the usual CTRL keys)'.
Done. And you're welcome.