Handbrake is an open-source multithreaded video transcoder available for
Mac, Windows and Linux. It enables you to pull from any DVD-like
source: Video_TS folder, DVD Image or real DVD and some .VOB and .TS
files. Output formats are MP4 and MKV – using Mpeg4 or H.264 (we prefer
H.264) codecs.

You can select chapters and subtitles.