If you sync your iPod with a different/empty library iTunes will only give you the option to copy your iTunes Store purchases directly from the iPod to the computer and everything else on it will be erased. You'll find details on transferring purchases in this article:
iTunes Store: Transferring purchases from your iPhone, iPad, or iPod to a computer
Purchased applications can be downloaded over again, see this article for details:
How to redownload purchased applications from the App Store
If you want to recover the music from CDs etc that is on the iPod and transfer it to your new computer there are a few things you can do. music from CDs etc.) there are a number of third party utilities that you can use to retrieve the music files and playlists from your iPod Touch or iPhone. You'll find that they have varying degrees of functionality and some will transfer data (such as playcounts and ratings), movies, videos, photos, podcasts and games as well.
A selection of iPod/iPhone to iTunes utilities:
Senuti Mac Only (iPod Touch & iPhone compatible)
SharePod Windows Only (iPhone and iPod Touch compatible)
TuneJack Windows Only (iPhone and iPod Touch compatible)
iPodRip Mac & Windows (iPhone and iPod Touch compatible)
Music Rescue Mac & Windows (iPhone and iPod Touch compatible)
iPod Music Liberator Mac & Windows (iPhone and iPod Touch compatible)
iGadget Mac & Windows (iPhone and iPod Touch compatible)
iRepo Mac & Windows (iPhone and iPod Touch compatible)
iPod Access Mac & Windows (iPhone and iPod Touch compatible)
TouchCopy Mac & Windows (iPhone and iPod Touch compatible)
I would also advise that you get yourself an external hard drive and back your stuff up, relying on an iPod as your sole backup is not a good idea and external drives are comparatively inexpensive these days, you can get loads of storage for a reasonable outlay:
Back up your iTunes library by copying to an external hard drive
One last thing, you need to take care connecting to an empty iTunes. Open iTunes first and go to Edit>Preferences>Devices and check the box "Prevent iPods and iPhones from syncing automatically" and choose Ok before connecting your device.
Once you have recovered everything from the iPod and your iTunes library has been rebuilt it will be safe to sync again.