I recently had the privilege of seeing an impressive presentation on reverse engineering Skype by two security researchers from EADS.  

These guys did some hard-core work on this.  In summary, the researchers found Skype to be a monolithic application binary built with extensive obfuscation and anti-debugging measures, as well as a proprietary wire protocol.  Unfortunately, while they provided great detail about their reverse engineering process, they were quite cagey about their overall conclusions, citing a vague confidentiality requirement.

They hinted at two concerns:

1. Skype periodically phones home, transmitting undisclosed data to other nodes.  Could this include personal information or other private data?
2. Skype nodes can be compromised, as can supernodes potentially, creating trust problems in the network.

Finally, although this isn’t mentioned in the slide deck, it was reported that EADS banned Skype from its networks as a result of this research.

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