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 for details. It certainly made people pause and think about what kind of shady stuff they were up to.

This is an excellent example of where user visibility into authorized processes could improve trust in software. Specifically, this software is ideal as a trojan horse; the user likely felt slightly coerced into installing it (install this plugin or you can't take part in this meeting / talk with love interest / remote family) and so they likely did so, possibly bypassing blessed trust sources. And even worse, the software is being granted privileges that are particularly ripe for abuse.

So this would lead a reasonably paranoid person to conclude that such software would be the ideal vehicle for privacy violation. Thus, if ever there is a software package for which a user ought to have visibility and enhanced control, this would be it.