What are advantages and disadvantages of converting to either m4v or mkv?
I don't use chaptering in my MKVs or MP4s, so I actually can't answer that question. I can say that the chaptering support of the MP4 container is a bit haphazard. Quicktime supports one standard, Nero Digital supports another, and so on and so forth. Almost all third-party players out there support either both or the Quicktime standard (for the obvious reason).
However, the biggest reason that
I use MKV over MP4 most of the time, is that MKV supports AC3 audio and the official ISO spec for MP4 does not. While you can actually encode virtually any codec into a MP4 file, if you use codecs that are out of spec, then some players will not support them properly. For example, if you use AC3 audio, Haali will still split it properly (meaning that MC can still play it correctly), but Quicktime won't play it, nor will basically any hardware player.
EDIT: Apparently, more modern versions of the
AC3 standard apparently officially supports MP4 containers, but the situation with the ISO spec for the MP4 container format is unclear. Either way, vendor support is still certainly not 100%. Many encoding tools won't let you do it, and even if they do, there's a fair chance your playback device won't work (especially if it is a hardware system). So, is it safe to use them? You
know the iPod player isn't going to support it, so what's the point?
Wikipedia has a pretty good comparison sheet here:
http://en.wikipedia.org/wiki/Comparison_of_container_formatsBasically, my method is this:
1. I rip or encode all of my "high-quality" stuff to MKV.
2. I use MC or another tool to recompress these to MP4 (M4V) when I need to use them on my iPhone or another hardware player that has limited capabilities.