What you can currently do is set "Minimize to the tray" in options, then run it as "bitcoin -min" so it starts minimized. \u00a0The only visible part will be a small (20x20) icon on the tray, which can be doubleclicked if you want to access the UI. \u00a0Note: there's a bug with tray icons sometimes disappearing on 64-bit Karmic Koala, not sure if it's from 64-bit or Karmic, it was fine on 32-bit Jaunty.
We didn't have time to implement the "Start Bitcoin on system startup" feature on Linux in time for 0.2 so it's greyed out. \u00a0I figured Linux people wouldn't mind doing that manually anyway. \u00a0I guess they need to know about the -min switch to do it right.
You can locate the data directory where you want with the "-datadir=<directory>" switch. \u00a0I know someone is already doing that to put it on a TrueCrypt USB drive.