Other open source MPEG-4 metadata editors:

mpeg4ip with mp4tags & mp4art - based on its own libmp4v2 (which is used in faac, amorak & more things all the time)
gpac mp4box which can set metadata (currently cvs can set iTunes-style metadata tags)
Audio::M4P is a set of Perl scripts to set metadata (and more)
mt-daapd contains an mpeg4 parser & allows setting artwork into files
bento4 is still in development and at the time of this writing, I wasn't able to make it set metadata
tg.exe is an older attemp at setting mpeg4 metadata with a number of limitations, but would be an excellent starting point
ffmpeg & VLC aren't editors, but both can provide some insight into how mpeg4 files are organized

AtomicParsley was started because I couldn't find a way to embed & extract multiple pieces of artwork into iTunes m4a files easily. Along the way, most of the metadata atoms that iTunes sets & uses in mpeg4 files were supported. The extension to video files exposed errors in the implementation of AtomicParsley, but ultimately resulted in a more compliant program. There need to be more tools for dealing with mpeg4 files - just as there is a great variety for dealing with id3 tags in mp3 files.

And I would urge would-be implementors to test on video files - nothing will break your code more than one of these behemoth files. An ffmpeg, an OpenShiiva (which itself uses ffmpeg, but with a 2nd mdat atom), an ISMA sample, an unmuxed mp4creator double-mdat/stco/co64 mongrel & a 3gp file with fragments work wonders lemme tell you. Hopefully this information will help others who decide to put their own spin on using mpeg4 containers. I know it would have helped me greatly if it was explained better (with a picture or two) when I started.