I'm pretty sure you could just use windows, and then just use the serial and parallel ports for input/output. The only real problem with that, is that you'll need a huge battery. Compared to a microcontroller, their power drain is insane.
If you do try to take the windows route, go for Windows 98 SE. You can strip it down to just the basic hardware interface, and then have your control program boot up, in place of explorer.exe