This page is an attempt to built a complete list of protocols found in use with MD devices (decks, portables etc). There are a wide variety of them used and not all is known about them and their limitations yet.
Net-MD:
Net-MD appears to be an extension to the AV/C Digital Interface Command Set spec intended for controlling IEEE.1394 (Firewire or i.Link) devices, though it runs over USB. It uses many commands from the spec, drops others and adds some of its own. There are only a few known Firewire MD devices: The MDS-DL1, MDS-LSA1, the unreleased prototype deck from Kenwood (shown at Comdex 98), and the VAIO PCGA-MDN1. Details of these devices command/control capabilities are murky.
Remote protocols:
Sony remote's seem to use 3 (or more) variants of a similar protocol for displaying text and controlling the attached devices.
Panasonic remotes.
Victor Remotes.
etc