The most simple back up method for bluray and dvd is to make a MKV with a program like make MKV and just rip the main movie and audio track of your choice.
This would lose menu's and all the extras, options and BD-Live crap but in doing so would reduce the back-up file size a little, retain 100% video and audio quality and ultimatley be easier to playback with free software or even windows media centre itself with the right codecs installed.
My HTPC is a Silverstone LC17 and can hold six hard drives.
Overall though, the main problem you need to think about is if you use your standalone bluray player, it going to be straight forward to play a movie.
If you go down the HTPC route, the experiance will never be as fluid.
You will have to overcome: -audio and video hardware and driver issues
Overcome media playback software and remote control issues
A/V Display sync with HTPC clock resulting and less than smooth playback that will vary by software player, codecs, hardware, back-up method and various video encoding types.
and thats of the top of my head.
Overall I still enjoy my HTPC and cant seem to let it go, especially for the kids movies that then wont get damaged, scratched, lent out and lost etc and they dont care too much if the video has the odd skip in it or if I made the back-up with AC3 audio instead of Dolby True HD by mistake.
But have to admit, when I put a disk in the bluray player (especially 3D) it just works.