3) The Frighteners (eac3to finds a structure, but it's picking up the wrong EVO files as the main movie)
Frighteners has an embedded Directors Intro at the beginning of the first main evo file, with a different format, which throws off eac3to (and ClownBD).
AnyDVD HD has a useful facility to modify the navigation .XPL files for HD-DVD since it copies the .XPL files to the Documents & Settings folder and allows one to edit them (when AnyDVD is not running). When AnyDVD is restarted, it will use the modified .XPL files for that title.
I won't go into the ins and outs of editing .XPL, as it should be covered somewhere on the net, but it is possible to remove all references to the Intro, so you only have the main movie appear in ClownBD. The only problem with this approach is that the chapter points will now be inaccurate, but this can be overcome by creating a chapter list and editing in Excel to subtract the length of the Intro from each chapter point and then write out the new chapter times.
Converting the primary soundtrack to LPCM and the commentary to AC3 permits the movie-only to just fit on a 25GB BD-R.
I found I had to use ClownBD to extract the video, main soundtrack, subtitles and chapters; ClownBD in a 2nd pass to extract the commentary; process chapter points in Excel; and then use TSmuxer manually to mux everything together.
TSmuxer seems incredibly slow though, taking over 1 hour to mux 25GB.
PM me for the movie-only .XPL and modified Chapter list.