I had a lot of trouble getting mission planner to run correctly on my linux 64bit debian sid system.
After lots of fiddling and tweaking I found installing ONLY mono-runtime and libmono-winforms2.0-cil makes mission planner run fine.
So for those of you wanting to run mission planner on debian (usually valid for ubuntu too):
apt-get install mono-runtime libmono-winforms2.0-cil
will probably do the trick.
After that you should assiociate it with mono to start from the file manager or just run
from the commandline.