A few months ago Bregalad released a utility called GBAMusRiper that rips the music from many GBA games into MIDI format with accompanying sound font files.
Apparently it even works with MOTHER 1+2, but only the MOTHER 2 side. And it works with MOTHER 3 too – apparently to the point that a hacker by the name of LuigiBlood was able to do some basic music insertion. Here’s a sample:
And here is another sample video.
I’ve never used this utility and I don’t know how one would go about ripping and inserting music, but if you’re interested, there you go!
Actually, I wonder if it’s possible to restore the quality of the GBA MOTHER 2 music using this utility as a reference…