Adobe Audition has awesome batch processing, infact I routienly take files that are recorded in stereo from a mono source (recorder won't record in mono) and strip out one channel in Audition for a part of my job.
Edit: How often are you wanting to do this, and what size are the files? If this is going to be a 1 time thing I could do it for you real easy, provided the file sizes aren't in the gigs.