It also appears that songs transfered from your synced songs to the ringtones using the native 3rd party iPhone application "SendSong" remain as well. You simply add your custom ringtones to iTunes as normal songs (mp3's or mp4's), sync, then copy them to ringtones on the phone using "SendSong". After this you can remove the ringtones from iTunes and re-sync so they don't junk up your playlist anymore.
The various iPhone applications that have been appearing really do add a surprising amount of functionality.