What is your end goal, quality or space savings and where do you want to play the stuff. I initially wanted to keep my library intact, so I ripped everything as ISO and for awhile it was nice. ISO allows keeping menus and all the little extras that are part of the disc. But, after 12TB I started to realize HDD space was getting too expensive, so I cut things down to just the main movie. Then after reaching 12TB again, I saw the need to compress the files which I am in the process of doing now. I decided on using the MKV container even though MP4 is more widely supported. There's enough software/apps out now that everything can likely play MKV and the container is more flexible. If I had to do it all over again, I'd first use
MakeMKV to rip the main movie and whatever audio/subs I wanted. From there use
HandBrake to shink the file and narrow down specific audio/sub tracks. The first pass of MakeMKV is pretty quick, HandBrake on the other hand, according to the amount of compression can easily take longer than the movie itself for something like a Blu-ray rip. HandBrake will also use up 100% of your CPU (GPU offloading is still being worked on), so having a seperate rig for these tasks can be handy. I'm still learning, but I have around 900 movies on my server (I use Media Browser). If you want to know more, feel free to hit me up via PM or Steam chat.
Edit: And for the record, yes, I own all of the physical discs that I currently have ripped.