If you can network the two machines together over IrDA, you could in theory use WebRemote or Glissando to control MJ. Windows direct connection over IrDA is pretty flaky though and not designed to work over distance more that a couple of feet.
You could also try downloading
Girder. It has an unsupported feature which lets you use an IrDA port as a remote control receiver. If it works on your machine, you could use it to convert remote signals from your PDA to keystrokes for Media Jukebox.
Probably the best option, if you have a spare $35 and a serial port, is to buy something like an
IrMan. This is designed to receive remote control signals and is directly supported my MJ and Girder. Lots of people on this forum (myself included) use this setup for their HTPC and can provide advice for setting it up.
Good luck