Well, one way I have found to work is to do the following:
1. Enable disc use on iPod from original computer.
2. Connect iPod to PC.
3. Make sure you can view hidden files.
4. Copy all hidden music from iPod (going to be in some cryptically named folder) into an empty new folder (on computer hard drive). Never mind the names.
5. Install iTunes and make sure that you enable the option of letting iTunes automatically organize your library (and copy all files into the library - its one checkbox I believe).
6. Point iTunes to other music files you got off the iPod, and let it work its magic. You should get a new library with proper names and organization, depending on ID3 tags.
7. If all fails, convert to AAC. The process of conversion and saving new formatted file will force iTunes to organize them in library.