Yes, with iTunes 5.0 you can connect more than one iPod at a time and work with them simultaneously. If they're not going to contain EXACTLY the same music, you will need to set one or both of them to use manual updating. My configuration:
1. 60 GB iPod Photo set to synch ALL music and playlists (no disk mode).
2. 4 GB nano set to synch only one playlist, "Songs on iPod nano" (no disk mode).