The M40 has a little better balance than the M50, though the 50 has more bass output and tightness. Vocals can seem more distant on the M50, though the M40 is also a "laid-back" speaker, and I've found I need to turn the treble up a smidgen (call the audiophile police!) for better clarity and mid/high openness.
If you listen to a lot of rock or instrumental jazz, the M50 is probably the way to go. If you prefer pop, dance, or classical, the M40 will likely be the better all-around choice. If you're predominantly a movie watcher, go M40s all the way and upgrade your surround choice to QS4s.