m4a containers for audio files have become quite common. Adding metadata via ffmpeg's -metadata mechanism works well with them, except for album art. The current solution is to use AtomicParsley:
On Ubuntu (14.04 at least), the atomicparsley package has problems. So we need to install it manually from its homepage:
Go to https://sourceforge.net/projects/atomicparsley/
Download and unzip it, for example to /tmp
Then move it to /opt, $ sudo mv /tmp/AtomicParsley-debian-0.9.0 /opt/
So far so good. Now, look up a jpeg image of a cover you want to add. And do:
$ /opt/AtomicParsley-debian-0.9.0/AtomicParsley song.m4a --artwork cover.jpg
This will write to a temporary file unless you use the undocumented --overWrite switch. Note that atomicparsley will not preserve the date-time-stamp! So make sure you stat your file first, and then correct the date with touch -d <date+time> song.m4a later on.