The easiest way to do this is to create separate playlists for you and your wife. When you plug in your iPod you can then select only the playlists you want synced and when she plugs in hers she can do the same, but you each end up choosing only what you want.

With the recent ‘Genius’ playlist option it’s pretty easy to pick a few songs you like, make genius playlists, and then save them to sync to your iPod.

If you rely only on checking or unchecking the individual tracks and enabling the ‘Sync only checked songs or videos’ option, you’ll quickly find that this is an all or nothing affair and you won’t have the control you’re after.

For more on playlists see the iTunes video tutorial from Apple:
http://www.apple.com/itunes/how-to/#video-playlists

@Phillip – Your function isn’t quite the same thing: iTunes->Preferences->Sharing “Share Entire Library” is great, but reading another user’s shared library only works while that user is both logged in AND actually running iTunes. Depending on how one shares a computer, this can be rather frustrating (switch user, log in, start itunes, switch back, access shared music…). And a bit of a memory hog, too.