NetworkPrivateMessage is a Bungee plugin that allows players on one server to message players on any server that is connected to that Bungee server.
I made a simple plugin to do this for my own (Upcoming) server and I though that I would share it here since I'm a nice guy.
The message command will send the designated player the message that you type.
/message <player> <message> (Can be either message, msg, m or pm as the command.)
The reply command will reply to the last person who you received/sent a message to.
/reply <message> (Also can be /r)