Not a good period of Skpye: few days ago its network shut down (allegedly due to a massive update and reboot of Windows), now a worm is spreading trough its network. These are two more hints about the importance of openess when adopting solutions that must deployed throughout the internet.
I'm not saying that Skype is insecure and that, for example, Google Talk (which adopts XMPP, an open protocol for IM and Voip) is secure. Behind software and services there are people, and people may do errors and even stupids things. Many "closed" vendors have systems for assuring software quality which are far superior than any open source project. However in the closed world the risk of some bug remaining silent for a long time and being exploited by some attacker when it's too late is far higher. When you are buying a closed solution, based on closed protocols, you can't have any assurance but the reputation of the vendor. In open solutions instead there often dozens if not hundreds of independent engineers reviewing code, specs, protocols. This is not bullet proof, for example SMTP is an open protocol and there are still many email clients spreading viruses and worms. However this is mainly due to poor client implementations or proprietary extensions (I bet everybody is thinking of Outlook...), not to SMTP itself (indeedm the design of SMTP can be blamed oly for spam).
Being SMTP open, you can chose among different client and server implementations, switch if you are not satisfied or experiment new solutions, and be sure that you will be always able to receive the email coming from any domain.
XMPP gives the same value: though a rather novel protocol, you already have tens of clients, servers and libraries available, different implementations that must work together, accordingly to public specifications. This usually means fewer problems due to malformed or unpredicted input as it happens in closed solutions, and, therefore less risks of attacks exploiting these bugs. And, finally, it means that at any moment you can chose the option better fitting your security needs, and still be operating.