Install Paint.Net on linux using mono

It looks like you've built and installed monodevelop from source - did you do the same for the dependencies like gtksharp? Since banshee and tomboy are broken, it sounds like you have a dependency shared between the broken programs, and that's an obvious candidate. Do CLI mono apps work?

From the MonoDevelop build documentation:

We strongly recommend you install everything from packages if possible. If not you, you should use a Parallel Mono Environment. Do not install anything to /usr or /usr/local unless you completely understand the implications of doing do.

If the other mono applications will only run from the installed monodevelop tree, and reinstalling packages hasn't helped, you might have a mess of extra stuff floating around that the source install has added which is interfering with mono finding its libraries, possibly with hardcoded paths into the monodevelop install.

My Debian-fu is not strong, but there should be a way of identifying files in /usr that dpkg doesn't know about, that might be a place to start.

MonoServerPath example.com "/usr/bin/mod-mono-server4"

should probably be

MonoServerPath mydomain.org "/usr/bin/mod-mono-server4"