Berkeley's mpeg_encode works very well, but it appears to have stuck at version 1.5b, and hasn't been updated for a few years. Obviously bugs have been discovered, and you can find patches on the web.

I found and fixed a couple of bugs in the param file parsing, if you use more than one shell command in the INPUT section, e.g.: 

INPUT
`ls first/*.mpg`
`ls second/*.mpg`
END_INPUT
The bugs cause crashes and incorrect calling of commands when a shorter one follows a longer one.

Here's my short patch to param.c

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