You can run iTLU through a GUI or from a console (which allows scripting). The following features are supported with iTLU:
- Adding new music or video clips to the iTunes library
- Removing entries from the iTunes library that point to non-existing files
- Synchronizing the iTunes library with one or multiple directories
- Updating iTunes track information with meta information out of the media files (for example ID3 tags in case of MP3 files)
- Updating your iPod (initiates a synchronization)
iTLU appears to be only available for Windows, but is completely free and comes with a short manual in English and German. If you want to clean up your iTunes, this is a utility that worked great for me.