[chris]

Your iPod can play:
AAC (16 to 320 Kbps)
Protected AAC (from iTunes Music Store)
MP3 (16 to 320 Kbps)
MP3 VBR
Audible (formats 2, 3, and 4)
Apple Lossless
WAV
AIFF

Can Windows media convert WMA to MP3? If so, do that, and then import all the files to iTunes/iPod - this way you can play the tunes in other applications besides iTunes...

Set the preferences in iTunes/iPod to reflect your want to use MP3, and things should be fine.

The process of converting is going to be time consuming regardless of what software you use, and what format you decide to use.