I've blogged about Amarok File Tracking before and there's a lot of information about it on the wiki. For those that haven't heard about the goodness of embedded file tracking, check out those links. There are a couple pieces of good news, and one piece of bad news.
The good news: in current SVN (and thus 2.2) the amarok_afttagger executable will also now handle FLAC and various Ogg-contained formats. Another piece of good news - the amarok_afttagger executable is now contained in the amarok-utilities package, and thus can be run on headless machines without X! And lastly -- AFT now works with user playlists, so you can move your files around (keep in mind the caveats if you're not using embedded AFT tags) and your playlists will always stay current, in addition to statistics and The Playlist.
The bad news? Something is currently a bit broken somewhere deep inside with Observers which means that The Playlist will only update with the correct new URL once (the metadata observers seem to die after that). This doesn't seem to be AFT specific but rather seems like a bug that AFT is exposing. Closing Amarok and reopening it will cause the proper new URLs to be in the playlist. I'm working on trying to fix that.
(Important note: it writes into the FLAC Xiph comment. This is the only metadata type actually required by the FLAC spec, and thus is the proper place to put it, but a lot of FLAC files incorrectly only have ID3v2 tags, so depending on the tagger you're using you may only see one or the other.)