It’s a laborious process, but here’s a pretty thorough walkthrough for using Jailbreak and iPhoneInterface to upload ringtones and custom system sounds to your iPhone.
What jailbreak does is (at a very high level) perform the first half of the restore operation that iTunes would, getting the phone into the powerful restore mode. It then issues a series of commands that modify the configuration of AFC to allow you to access the full filesystem while still presenting the same interface to iTunes (so as not to break syncing).
After that, iPhoneInterface allows you to interact with the phone using AFC to upload and download files.
Once you’ve run Jailbreak, you have quite a bit of access to the filesystem with iPhoneInterface. When you’re comfortable with this hack, you might want to poke around and see what other files can be tweaked to add new behaviors, themes, or functionality to your device.