The Protocol Filter is an application layer packet classifier. It can be used to block unwanted traffic from your network - the most common being to ensure employees, students or end users are using their Internet access for its intended use.
The service attempts to identify an application as data packets pass through the gateway and classify them according to known protocols. If successfully identified, user sessions can be blocked based on an administrator's preference and/or policy.
"Essential app on ClearOS if you're interested in increasing employee productivity." (EN)
With more and more applications like file-sharing and Internet Messaging abusing standard ports designated for legitimate services, the protocol filter app can be a valuable tool in an administrator's desire to control what types of traffic are allowed on the network.