You can probably put a sniffer and see what ports/protocols are used by Skype. Atleast I can tell you this, that skype calls are encrypted. (AES)
Skype versions 1.0.x have some vulnerability in the code, so if your users do not update their versions to 1.0.0.100 malicious users from internet can compromise the user's pc and then may be hack your network from there.
Sankar Nair
UC Solutions Architect
Pacific Northwest | CDW
CCIE Collaboration #17135 Emeritus