SuperSync is a cross-platform application that allows you to sync two separate iTunes libraries. I actually have this problem as I am planning to set up some kind of central home music server, but my family has a couple of separate libraries. Unfortunately, there are a lot of duplicate songs between the libraries, so just mashing them together is not really feasible. SuperSync allows you to compare the two libraries and only copy over what missing. In addition to the syncing function, SuperSync allows you to access your music library from across the internet, e.g. accessing a home computer while on the road or at work.
SuperSync is available for Mac and Win (and, to be frank, it shows). Licenses come in multi-packs, temporarily on sale for $29.00 for two.
[Edit: I've heard some reports about problems with this software. As always if you try any software of this sort, be sure to backup!]
SuperSync: iTunes Library Syncing
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