So, I'm trying to package my Python app, Virtuam. My question is simple: how can I set the commands which run when I remove the program using apt-get?
You will need to use maintainer scripts to do things during the removal of your app (specifically prerm and postrm).
You may want to take a look at Debian packaging policy http://www.debian.org/doc/debian-policy/ch-maintainerscripts.html
Below is an example prerm script that I had previously used when removing the mythbuntu-repos package, in order to remove the added repository and key information as well.