I don't know whether this is still the case but Skype used to use some of the most advanced anti-debugging, runtime code obfuscation, etc etc methods of its tim

I don't know whether this is still the case but Skype used to use some of the most advanced anti-debugging, runtime code obfuscation, etc etc methods of its time for no obvious reason. See http://www.secdev.org/conf/skype_BHEU06.handout.pdf http://www.secdev.org/conf/skype_BHEU06.handout.pdf for details. It certainly made people pause and think about what kind of shady stuff they were up to.