HandBrake

Oops… Not sure if you are adverse to CLIs but if not you could try ffmpeg (exists for windows!). There might be a GUI for it. If you just want a transcoded aac stream: ffmpeg -i in.mp4 -vcodec copy -acodec aac out.mp4 -acodec copy -newaudio If you want to have 2 audio streams: a transcoded aac strea...

http://code.google.com/p/subler/ alows muxing and can transcode ac3 to aac