I used the current version of makemkv to rip all of my dvds about 5 or 6 months ago and I have been happy with the results. No compression but it does let you select which audio tracks and subtitles you want to put into the .mkv container. It is very easy to use and I had good success with using 2 dvd drives and ripping 2 movies at a time too two seperate hard drives.
I did have an issue with movies that were recorded with older styles of dolby surround. 4 channel dolby surround (wild audio sync issues with one movie) and 2 channel dolby surround (audio gradually becomes more and more out of sync) but I believe these issues have been fixed in more recent updates. dolby 5.1 was always spot on as was dts as were some of the older mono track dvds I had (Caddyshack!). All these issues were worked around using dvdshrink and then makemkv or just using handbrake.
I have little personal experience ripping blurays with makemkv but a friend of mine had some issues with audio sync, although i believe his problems had more to do with his inexperience setting up an i3 setup for home audio and not having hdmi capable receiver.
Give a couple of different audio and media formats a try with the different ripping options to see which programs you like the best before tackling you whole library. The trial time is well worth it!
EDIT: If you want, I could try ripping some of the movies that i had issues with with the newest makemkv and see if any of the sound issues have been fixed. Just let me know.
also, .mkv is just the video container. You can have h.264 video inside of it from a bluray, or if you are ripping a dvd you will end up with mpeg video inside the .mkv container.