Here's my experience:
GameYob has programmable shoulder keys so select can be assigned to L, which is very useful indeed. LameBoy doesn't seem to be able to do this, which makes me sad.
LameBoy seems to have a much smoother wav channel, with hardly any clicking, whereas GameYob clicks a lot on wav. Also with high speed vibrato.
In theory I could write tunes on GameYob and record from LameBoy, but that is a faff.
Anyone else got a preference, or anything to add?