if you didn't buy them from itunes (specifically, they're not DRM'd), then winamp, with ml_ipod, will nicely take all of your tunes, transfer them into a named, standardized directory structure, in one go, for free. Its also vastly better (imo) than itunes at managing your music in the other way, too.
If they are DRM'd, then you might be able to get apple to do something (some DRM methods allow copying once or twice, to cover this exact scenario). I'm not sure of the specifics of the Apple solution though.
H