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.)
"there exist open-source tools, running on UNIX-like OSes, for writing this file as well."
Actually, writing it is pretty trivial, and there are lots of windows programs that can access, fill, and even copy songs FROM an ipod. RealPlayer (if you're silly enough to install it) takes over your iPod. There are some standalone programs like Anapod. Personally, I use a Winamp plugin that lets you access your iPod from Winamp, and drag-and-drop files from your harddrive onto your iPod through that interface, since iTunes insists on only letting you put songs from your permanent library on iPod - a lot of my mp3s are on CD-ROMS.
Apparently the next-gen ipods will be able to play Oggs too (well, the hardware will be able to, but you'll probably need to install Linux to get software that plays the files).