My process is a 2 stepper and adds a couple of extra steps to make sure I get exactly what I want every time.
1 - Run the BR through BDInfo and identify the main playlist with the movie.
2 - AnyDVD HD running in the background
3 - Load the main playlist with TsMuxer (free program) and choose the streams that I want to keep and strip the rest out. Rip to a single .m2ts file with Tsmuxer
30-45 minutes later you'll have a single uncompressed movie file that will play back on almost anything, but the size could be anywhere from 13GB to 45GB. For my handful of favorites like Gladiator, Heat, Fight Club, etc., I just store them like this. For everything else, I go to the next steps and shrink the size.
4 - Load .m2ts file into Handbrake or Ripbot264.
6 - I usually encode to an .mp4 with 2 audio tracks. The first is a 2-track .aac (128kbps) and the second is a 6-channel .ac3 (448 kbps) or DTS track. This usually guarantees that it will playback on almost any device.
5 - h264 settings: I downscale most movies to 720p unless it is something that really benefits from being in 1080p. I use 2-pass and a bitrate of 2200-2500kbps on 720p and 6000kbps on 1080p. The advanced settings are up to you and can have huge affects on quality but also how long the encode takes. I usually plan on 8-10 hours with and AMD Phenom x4 955. I usually end up with 3-4GB 720p and 7-8GB 1080p files that look great on my 50" plasma from 10 feet away. If my TV were larger or I sat closer, I may be more liberal with the bitrate.