I also use my iPod to record sounds, & I must admit that converting them to wav format is quite tedious, especially with hundreds of sounds.
On my old bank, I used Audacity, & I sat there for about 2 hours opening up every sound and exporting it as a wav into a new folder. Nowadays, since I now have a Macbook, there's this application for Mac that I use called Music Converter Pro which'll convert multiple sounds to one format, usually in a matter of seconds.
So, basically, you could try to find a free downloadable equivalent to Music Converter Pro (which isn't free btw, it was like $10), use Audacity to convert them by hand, or find an online converter & sit there converting each file. Annoying, I know :/