Part 1
I'm looking for a program that I can create a single VOB file from a DVD. Sometimes I will need to decrypt, many times the dvd's will not be protected. I have tried with success dvddecrypter - should I also use a "decryptor" if their is no decryption necessary (just a way to end up with one file)?

It would also be nice to be able to easily isolate the subtitled segments as well.

Part II
In theory should the audio quality be exactly the same comparing the dvd with a vob file that was processed with dvddecrypter (or a similar program). I understand that technically if I am not applying compression that it should be the same 1:1 quality, but a test that I ran had the vob audio file as slightly muffled.
thanks in advance!!

DVDShrink does all that, and more.

Audio is not compressed in DVD-video when you compress the video. If you're using some kind of a transcoder to convert DVD-Video to MPEG2, it may well be transcoding the audio to MPEG audio or something else.

All you have to do is use Shrink to rip the DVD with whatever audio stream, or streams, you want. With Shrink set to create one VOB. Then re-name that VOB to MPG and you're set.