MTP appears to be based on the Picture Transfer Protocol used by some digital cameras, only with some Microsoft extensions, and is tightly integrated with the Windows Media Player; it is currently possible to hack gPhoto, a command-line PTP client, to talk to at least some MTP players. There is some doubt over whether or not this infringes on patents. Users of pre-XP Windows systems, however, may be out of luck.
For Penguinheads and other Windows refuseniks, the Apple iPod is apparently still usable. It looks like a USB Mass Storage device (or a FireWire hard disk), and can be copied to/from, though requires music files to be indexed in a proprietary database file onboard, which iTunes writes; there exist open-source tools, running on UNIX-like OSes, for writing this file as well. (Disclaimer: I've never owned an iPod and so have no experience of how useful or clunky it is to use without iTunes. My way of filling my MP3 player involves mounting it as a disk and copying files or directories to it.)