iPodBackup is a shell script-turned-application (via Platypus) that backs up your home folder to your iPod using the open source backup utility rsync. Combine it with Do Something When to have fully automated incremental backups to your iPod, for free!
You can customize a list of items to be excluded by simply dragging-and-dropping them onto the app. By default, the Music folder, as well as certain cache folders are skipped, in order to prevent duplicating your music and because caches are a kind of stupid thing to backup.
Please see the iPodBackup info page for more usage info, as well as a detailed guide describing how I made the app.
A note for first-time users: The first backup can take quite a while, especially if you use an encrypted disk image! Subsequent backups will be much faster, as only files that have changed will be copied over.