Well. Right now I primarily rip to BluRay folder structure (main movie only) using AnyDVD + Clown_BD. This allows me to capture forced subs with ease and has been most compatible with the various players I use.
As far as mkvs, I actually am still a little bit old school and use Clown_BD + mkvmerge
However, I think BluRip is probably one of the best solutions out there (requires AnyDVD)
MakeMKV is great and free as of now (it decrypts without the need for ANyDVD). The only thing I don't like is it doesn't set the forced flag for forced subtitled.
Here is a list of the various mkv articles I have written
Hope that helps