Isn't it compatible with the Microsoft variants? I mean, isn't that the point? Shouldn't you be able to build on Microsoft tools and then compile on Mono for other platforms? Or am I completely missing the boat?

That is exactly the point, however last year I had an existing .NET build that I wanted to port over to linux - it was developed with VS2005 / .NET 2, so should have been fairly trivial to port.

The issues I ran into were many (eg windows forms, data access being not or only partly implemented) so I just gave up and ran the original .NET in a windows virtual machine, rather than mangle it to work with gtk#.

So in principle it is an ideal idea that in practice has many issues due to MS driving .NET development and MONO having to play catch-up and then attempt to mangle the windows-specific code to be cross-platform. YMMV.

It's doing quite well, there are some areas that they aren't really focusing on, but before porting try running this tool: http://www.mono-project.com/MoMA It's a migration analyzer and it will help to identify incompatibilities.