MediaCoder – Converts and encodes almost every kind of media file known. This particular program has somewhat of a steep learning curve but is very powerful once mastered. This program will also convert to ipod format although Videora is more straight forward and user friendly.
Xrecode – Converts audio files. Has a much simpler user interface than mediacoder and it works well for recoding audio files of any type. This program excels at splitting (for instance) a single file album into single songs. In my case, I downloaded a single .ape file that had a whole album. I used Xrecode to split it into single songs. Highly recommend.