This one is highly recommended by the alt.comp.freeware newsgroup. I have not used it personally yet, so am not absolutely sure abot batch processing) I'll check a couple places.

PROGRAM_NAME: XMedia Recode
VERSION: 2.0.6.7
RELEASE_DATE: 2008-9-2
HOMEPAGE: http://www.xmedia-recode.de
DOWNLOAD: http://www.xmedia-recode.de/download.html
WINDOWS_OS: 2000/XP/Vista
OTHER_OS: -
DESCRIPTION: XMedia Recode is a video and audio converter which
supports nearly all audio and video codecs, but is geared towards
video conversions. It is very easy to use.
REMARKS: Website is in German, and so is the program when you first
run it. Go to 'Optionen' and change 'Sprache' to 'English' (if you
like). Then restart the program.
Program settings and all other files are in the program folder.
COMPANY: ---
AUTHOR: Sebastian Dörfler