I'm inclined to agree with Matt on this. The quality differences between PCM and Dolby Digital are audible on good equipment (not even great equipment). If the format of the original soundtrack is stereo PCM with Dolby Surround and there's ample space on the disc, I don't see a reason to re-encode it as Dolby Digital. The Dolby Surround mix in PCM format with a Pro Logic IIx decoder is definitely superior to the 5.1 mix on the 2004 DVDs.

I think my dream homebrew trilogy would be ocpmovie's video with PCM audio from the laserdiscs.