I've done this with my wife's iPod and our iMac. We both have our own accounts on the iMac, and use mine as the main account. As she likes only a portion of my music, she naturally only wants a particular selection - and vice versa!
From memory, you need to move your iTunes library to a shared folder (not the application, just the library!). Then, logging into your wife's account, boot up iTunes. There should be no tunes linked. To link only those she wants from the shared library, there's an option to Add To Library (in the File menu?). Simply select the music she wants in her library. Only those tunes will appear in her iTunes library on her account and these will sync with her iPod.
To add tunes to her library only, import as per normal while in her account. This will add the tunes to the 'master' (shared) library, but only be available on hers (unless you log into yours and then Add To Library).
This saves doubling up on music files, saving space.
It can be annoying when you both want the same music, though (having to import in one, then log out, log in and Add To Library in the other ...)
At least, that's how I remember it working!