Search MP3/Ogg files by tags/parameters from the command line

For MP3, try eyeD3, found in this SO answer.

  --add-image=IMG_PATH:TYPE[:DESCRIPTION]
                      Add an image to the tag.  The description and type
                      optional, but when used, both ':' delimiters must be
                      present.  The type MUST be an string that corresponds
                      to one given with --list-image-types. If the IMG_PATH
                      value is empty the APIC frame with TYPE is removed.

For Ogg, there's vorbiscomment. It doesn't support loading image files out of the box, but a cover art tag in Vorbis is just an image file encoded in base64, stored in the COVERART tag and its mimetype in COVERARTMIME - something like

coverart=$(base64 $jpegfile)
vorbiscomment -a -t 'COVERART=$coverart' -t 'COVERARTMIME=image/jpeg' $infile $outfile

I've used id3v2 before and found it to be quite good.

There are some others according to aptitude: id3 and id3tool. Assuming you have a Debian-based system: aptitude search id3. I'm sure other package managers should have a search facility.

I'm not sure these will be able to do everything you want (by which I mean I don't know anything about Lyrics3 and APE), but you can take a look. Certainly id3v2 has -s, -d and -D flags to remove id3v1 tags, id3v2 tags, and both, respectively (according to its man page).