I dislike that MJ pops up in front of any window in which I am working, should I make or receive an MJ call. I looked for solutions, to which I found complicated AppleScripts, etc. Finally, I found a neat piece of FREE software for Mac called Afloat, which interacts with the Window options menu within each window you might be in. You can set the window to be "Afloat", in which case that window will remain on top no matter what goes on behind it (until you close the window, of course). I think it's brilliant, and much easier than having to type Control+H, or right-click on MJ and Hide each time.
Here's the link:
http://infinite-labs.net/afloat/
MJ Window Pop-Up Distraction
Moderators: Bill Smith, Pilot