A protocol is a method that is used to send, receive, and handle information over a connection. Common protocols viewed from the browser include http, https, ftp, and mailto. In order for you to view information sent over a specific protocol, it must be registered. If you enter a URL for an unknown protocol (foo) in the Location Bar, you will receive a message such as, Firefox doesn't know how to open this address, because the protocol (foo) isn't associated with any program or, in Mozilla Suite/SeaMonkey, foo not a registered protocol.
Once registered, the protocol can then be handled by the program you specify, such as your browser or a third party viewer. This means that a hyperlink ( e.g. foo://fred) can use the handler for protocol foo to open the file named fred.