Shoutbox

You are right, commands such as sounds are sent through normal messages.  These relate to either a sound stored locally as a default sound or one in the scripts database that matches the id sent.  For the sounds database go to www.msgpluslive.net/sounds/ or mpsounds.net as these are both great for the information.  Any information that is sent between 2 people is done through text in the chats and you should be able to start understanding all the special symbols after you see the same type of message used a few times.  there are the likes of /me as well for actions and /ping to check if someone has plus installed.  Oh and sounds are sent to the database and then to your contact I do believe (I might be wrong on this fact, I personally haven't had much to do with it at all).

As for what Plus! is coded in, it is done in Visual C++ I do believe and the single person who codes it uses the name Patchou.