I was fiddling with this to get my Le Mans music onto the iPod this year. I didn't find a way (I took the laptop itself anyway).
However...
Do you use XP, and if so, do you and Mrs Diesel have separate accounts on the same machine? If you have different accounts then I imagine you could instal iTunes separately under each logon (for that logon only) and in that way you can have separate iTunes libraries. Not sure it would work, but has to be worth a look?
Or maybe you could use a shared music store, but use Playlists to manage what gets updated to the iPod. I think! (Manual sync must be an option???)