what is the best program to use for muxing MPEG?
 

I've noticed that most people here recommend BBMpeg for multiplexing so I wanted to ask why is it better than other programs, like TMPGEnc (if it is), what's the difference, and what is the best program to use?

I personally do all muxing with tmpgenc but some people have reported problems with the playback on their standalones. And it seems that no problem was ever reported with something muxed by bbmpeg.

That is why and how bbmpeg can be considered as "best" one.

I've never encountered any troubles with TMPGEnc, so I guess there's no reason not to keep using it.

If I remember it correctly, TMPG will cause errors when muxing SVCD out of specs. I don't know about VCD (with my player I have to use mpeg2), but I think it should work the same way.
For example try muxin an MPEG2 VBR 300-3000 with audio at 224 as SVCD. This will produce many errors, mainly video buffer underflows that will lead to some video freezes or even to a complete unplayable file.
I believe that this is caused by the fixed mux rate (bytes/sec) that TMPG have when muxing SVCD (or VCD) standard. You can change this setting with BBmpeg… leaving it at 0=auto this problem will never happen.