Lifehacker has an app I've been searching for... the MP3 to iPod Audio Book Converter. (From this list of 20 iPod utils.)
I use Melodycan
It converts different audio & video file formats. Such as wma, wmv, m4v, mov, aac, ra, aa, mp4, snd, aif, m4p, rax, wav, ogg etc. Moreover MelodyCan converts audio books, any format Media Player, any format QuickTime Player, any format Rhapsody or RealPlayer supports. It`s very simple to use. Now I can download YouTube files to your PC with MelodyCan YouTubeRipper.
Conversion speed and quality is very good. Also I noticed when playback window is partially obscured it doesn’t affect converted file. So as for me MelodyCan is a great solution to convert protected files - legally.