I’ve been ripping a lot of my personal DVD and Blu-Ray collection to be put on my NAS system instead (see my multiple posts about how XBMC is awesome). I usually use Handbrake or MeGUI to encode to xd64 MKV files and preserve the commentary and different audio tracks. I also use AnyDVD HD (Yes, I actually bought it) to take care of any copy protection on the disk. It is amazing and anyone who wants to rip movies (espeically Blu rays) should use it.
The main problem for me, is hardcoded letterboxes. When you get a Blu ray disk, you are expecting the highest resolution video you can get (until 4k gets popular). Which usually mean 1920×1080, or 1080p. But most disks I’ve found have hardcoded letterboxes so the actual film is only a fraction of that. For example, I just bought the Bond 50 Blu Ray collection, all the James Bond movies on Blu Ray in one box. Every disk, even the newer ones are NOT 1080p, they all have hardcoded letterboxes that take up about 100px or so on the top and bottom, losing about 200px total. When removing the letterboxes on rip (most programs do this automatically), the movie is actually only 1920×816. So many blu rays do this and it’s driving me nuts.