There's a free program called Senuti. Download that, and use it to transfer your music into iTunes. Once it's done, you can restore your iPod (which will wipe everything), and will install the Mac formatted software. When this has finished you can sync everything back onto it as it is now in your library.
However, Senuti only works with videos, podcasts and music - anything like games (aside from the ones that were already installed on it), notes, etc. will be lost.