Skype is in trouble again, this time with a company called StreamCast Networks (the developers of Morpheus). StreamCast claims that the P2P technology developed for their Morpheus software is being used without permission by Skype for their telephone services, and thus has filed a lawsuit against them. In a unique twist of things, Skype didn't directly do anything - they continued to operated like normal, while other politics resulted in the infrastructure supporting Skype changing hands.
Skype is already in other legal trouble, so it seems plausible that Skype may pull a RIM-like move and attempt to move their service to a new protocol or find another way around using the existing FastTrack network. Then again, using a P2P network for a paid Internet phone service seems a bit fishy. Time will tell!