Certain tasks are impossible to perform with the standard Bukkit API and may require working with and even modifying Minecraft directly. A common technique is to modify incoming and outgoing packets or to inject custom packets into the stream. This is quite cumbersome to do, however, and most implementations will break as soon as a new version of Minecraft has been released, mostly due to obfuscation.
ProtocolLib is a library that allows read and write access to the Minecraft protocol. It handles most of the overhead required with reflection and channel injection and provides wrappers to simplify packet modification. It is updated with most Minecraft updates so, ideally, individual plugins don't have to. ProtocolLib often doesn't need to be updated for minor updates, especially if there are few code changes (i.e. the 1.8 security updates)