I've been using AnyDVD and HandBrakeCLI for converting my Bluray collection to MKVs for use in XBMC for a few weeks now. I've got the process down fairly well. Here's what I use in case you are interested:
Rip the Bluray to an ISO with AnyDVD on my windows box to my server (Ubuntu powerhouse).
Run the following commands on the server to find the title information and audio tracks I want:
mount /media/bigdisk/video/ISOs/up.ISO /media/Bluray -o loop
HandBrakeCLI --scan -t `HandBrakeCLI --scan --main-feature -i /media/Bluray 2>&1 1> /dev/null |grep "Found main feature title, setting title to "| cut -d" " -f8` -i /media/Bluray
The first command mounts the ISO (windows equivalent to using clonecd...)
The second does two things, first, in the section between the `s, it looks for the main title, then returns the details of that title, like languages for the audio and chapters, as well as the title number. I then make note of which audio tracks I want and which title it is.
Then run the final command below:
HandBrakeCLI --format mkv --markers --encoder x264 -b 8100 --two-pass -a 1,4,5 --aencoder copy -x ref=1:bframes=0
ubq=6:mixed-refs=0:weightb=0:8x8dct=0:cabac=0:weightp=0:me=dia -i /media/Bluray -o /media/bigdisk/video/Movie\ DVDs/Up.mkv --title 93
This creates ~9GB file for a movie with acceptable quality for myself and my wife on a 1080p projector on a 110" screen, so fairly good.
The parameters of these can be converted to the windows Handbrake if needed; I just prefer batching my conversions on my powerhouse.
My next task is to figure out how to easily rip the subtitles to add for my foreign films