MediaBox currently reads embedded cover art from MP3 ID3 tags. There is no tag parser for mp4 yet. The tag parser reads ID3v1, ID3v2 (up to 2.4), FLAC, and Ogg comments.

EDIT: I'm not quite sure if release 0.95 already supports reading FLAC tags. The current developer version from SVN does, though, and so will the soon-to-be-expected release 0.96.