Which software to batch join videos and add a chapter for each?
Ever since the fall of Visual Hub, there have been several generations of programs that have taken up the sourcecode and tried to remake the magic.  Visual Hub was awesome at stitching files together, sad it no longer works.  Film Redux was a fork of VisualHub, but has since been abandoned also. You can still download FilmRedux for free, however I can't get it to process any of my files. It may just be a configuration issue on my machine, you may have better luck.  

Your Mac should have come with iMovie, otherwise it's at the Mac App Store for $15.  I found this comprehensive guide to iMove '09 and the section on markers is still relevant to iMovie '11.  The drawback is you'll have to add them manually, but that shouldn't be too much trouble.