No Problem
When I switched from PC, I first used the ipod as an external hard drive and transfered my files. The iPod was formated for windows and it was not a problem. But at the time all I had was a 4GB mini. The process was very very slow.
I then did this which may be the best alternative, you can actually turn your windows machine on to share folders. You can then send the files wirelessly over the network to your new mac. Once you start the transfer you can leave and come back in about an hour or a period of time and it will be done.
You can keep all your files on your PC also.
Hope this helps