I am running Ubuntu 9.04 64bit. One thing I noticed is that the integrated debugger is behaving quite flaky for the included Monodevelop 2.0 package. After some research, it turned out that a lot of people are having similar issues.
So I followed the instructions given in these two blogs: Install Mono 2.4 on Ubuntu,
Building Mono and MonoDevelop from source on Ubuntu 9.04 64bit to re-install Monodevelop 2.0 and its dependencies from the source.
One thing you will need to pay special attention to is that for the monodevelop-debugger-mdb-2.0 to compile successfully, you will need mono-debugger version 2.4, instead of the latest version 2.4.1. Otherwise you will receive an error on Thread.AbortInvocation as there is a breaking change in mono-debugger 2.4.1 which added a parameter to the method (see mono debugger 2.4.1 change log).