For video transcoding, there a number of programs I use, depending on the situation. Some of the most frequent are
Handbrake, mkv2vob, Multi AVCHD, and VLC
However, for changing container formats, without transcoding audio or video, I have only been able to find mkvmerge for remuxing to the mkv container format, and mkv2vob, as well as tsMuxer, for remuxing to the ts or m2ts container format.
For going to another container, like mp4, I am stuck with actually transcoding to mp4 in the aforementioned software.
So what I am looking for is a program that can remux video to a number of different container formats, including mp4, in batch mode.
The use case is for playing on some different set-top media players. Playstation3 will play just about anything except an mkv. My solution has been to remux to m2ts, but transport streams add ~10% to the filesize. I have a big hard drive, so its not a huge issue, but it seems needless. My parents have an older Western Digital media player (pre-WD TV) that will play a few formats, but really is happiest with an mp4.
This doesn't seem like a very tall order, but I haven't found one yet.
Any suggestions would be greatly appreciated.