Shoutbox

Like I said, either by contacting the computer of your contact directly like in a P2P (point to point) connection, but that is very hard to do.

Or either by simply sending your own commands to your contact. Such scripts recieve the commands via the conversation, so it would still be visible though... But the visible 'text' could be whatever you want, for example encrypted like riahc said, so that the humans can't read or interpret it...

In whatever case, both you and the contact need to have a script. And since both need to have a script, why would you still send 'invisible' stuff. I mean, your contact must install the script, so he knows what the script does and why he has installed it anyways. You might as well just send 'visible' text/commands in that case since there is nothing to 'hide' or 'secret' about it anymore.