Although there is no proven way to completely protect yourself from the money hungry bastards that want to limit and control the P2P networks, there are some ways that you can protect yourself.
First of all, don’t share your entire hard drives. I have seen people sharing their entire C: drive. (Windows users of course)
Second, use some sort of program that will block connections to and from servers and clients that are known as fake, bad, corrupt, or just some unknown that seem suspicious. Two programs I know of are… Protowall and PeerGuardian.
After you have an IP Blocking Program, you have to keep it updated. There are probably many more, but I use Blocklist Manager which can update block lists for eMule, PeerGuardian, Protowall and many more.
Third, if you are sharing lots of files, DON’T leave your P2P program running 24/7 if your not downloading anything!