I'm likening media monkey lately
 

I've been comparing media monkey and itunes lately and there are things I like about MM more than itunes. I'm still on the fence, mainly since, as an older dog, I am new trick averse, and I get flummoxed by all the bells and whistles of MM, but it is slowly gaining favor.

So MM can be used to replace iTunes for syncing iPods?

yes, and it has the feature to automatically convert incompatible or extra large files into 128k bitrate compatible files

My solution has been to search for m4a files, move them over into a "quarantine file" and then never look in that folder ever again.