audio in MP4

[Drsss]

I'm trying to backup a DVD movie. I've recoded the video to AVC using x264 but I'd like to keep the AC3 audio stream. My first idea was to mux those two streams (video and audio) together in an MP4 container. Normally i use mp4box for multiplexing but it doesn't support AC3 audio. I've downloaded the nero digital trial version but I can't find how to mux those streams together using that software. I've also tried the trial version of Elecard XMuxer Pro but that crashes when I attempt to add the raw AC3 stream.
I've read that Matroska supports muxing AVC and AC3 together but I can't find a CLI muxer for matroska. I also prefer MP4 because it's a more standardized container.

So here are my questions:
Is there a way to mux AC3 in an MP4 container? (and how)
Is that procedure recommended in terms of hardware/software support, standards compliance, etc.?
Is there a viable alternative for AC3 that can be easily muxed into an MP4 container? (preferably lossless compression, 5.1 support, dynamic range compression support, etc.)
Are there any alternative container formats that support AVC+AC3 (and subtitles)?

I've read the FAQ's and i've searched around but haven't found any conclusive answers yet.

[J_Darnley]

From what I have read AC3 streams in an MP4 container is not standard compliant, but then I'm not familiar with the MP4 container.

Matroska is the alternative container for almost everything. The CLI tool most often used for muxing probably is MKVtoolnix. The thread about the tools is a a little further down in this forum. MKVmerge id what you want, the package even has a good GUI for it.

http://forum.doom9.org/showthread.php?t=120648

The basic command would be:

mkvmerge -o output.mkv audio.ac3 video.file