Starting with 9.04, Ubuntu ships with a program called Janitor. Janitor is meant to find unused files and packages, giving you the option to delete them and save space. Good idea in theory, not so good in practice.
I gave Janitor a spin and it ended up deleting programs that I was using, among them VirtualBox and Skype! Alright, a large part of it was my fault, because I should have read the instructions and the options carefully. But still...
...use Janitor with care. Or don't use it at all.
Apparently, I'm not the only one who feels this way.