Over the years, the case whether Skype is appropriate for the enterprise has regularly been brought up. I just read a news article talking about a recently released trojan that intercepts Skype voice conversations and is based on code that was developed 3 years ago.
From this first article, it sounds like the malware gets installed onto a target computer, and then records all voice communication that Skype attempts to make. It is unclear if this includes call information routed through a system designated as a supernode.
Regardless whether it does or not, keep in mind there are governments in this world that would outlaw Skype if there was no way to intercept those calls (even in 2006!). And they typically “allow” Skype. That alone should be enough to give you some clues…