hi there are a load of programes to do thiswww.snapfiles.com or ilounge.com
I have the same thing happen, number of things tried, most sucsess (my music collection is bigger than IPod so dint want tot do what your doing just incase i lost anything.
1, do a search for all your music files .mp3;.mp4.m4a and any other formats you may use and copy them all in to a single folder. go in to Itunes and delete the library (dont choose remove from harddrive :-).
then with your new empty itunes import the folder you copied everything to. takes a while but works well.
If itunes is vastly diffrent to your Ipod I have had it it ask me i iwished to copy content from ipod back to Itunes..
ipod is a hard drive, just plug it in and copy the music off, the software makes it easier and you can se what your doing but it is all accessable with out software.