A group of German programmers has figured out the MiniDisc communication protocols, and they’ve written software that allows certain units to communicate with computers without the SonicStage software layer. The nuts-and-bolts are here, and a streamlined installation for Ubuntu is available here.
There are packages available for the Macintosh, and a limited set of protocols are available for Windows computers (owing to an outdated version of libusb on that OS).
The graphical interface is called QHiMDTransfer and automates most of the capabilities. The most important feature so far is the ability to upload PCM and mp3 audio from the MiniDisc unit to the computer. So far, only the newer Sony MZ-RH1 is supported.
This is something of a godsend for me, as my recordings are dumped from the mixing board to MiniDisc. The software now allows me to upload them directly without having to reboot into Windows and copy the files across partitions.
Thus far, download of tracks from the computer to the unit is not supported, but a hack to allow it is in the works. You can keep track of development here.