Regarding folders and stuff, I personally like it just the way it is, symlinks under linux (and I guess junctions in ntfs, but I havent tried it) takes care about everything anyways. If you create a folder for each movie with just a single symlink (the symlink can be named "movie" to make things more intuitive) to the movie file, be it m2ts, ts or what ever. I did a script that symlinked all my .ts movies this way back in the tvix 5000 days. I run it once a day, and it would traverse the whole tree, deleteing stale links and creating missing ones.
In this symlink "shadow folder", Guy's files are also stored.
The other benefit with this is that you can have one movie folder (by the looks of it) to navigate to from your Tvix, but the actual files scattered among many drives, as they get full. If you like, you can also do multiple symlinks that sorts the movies in different ways.
i.e. main movie directory has
"Movies sorted by genre"
"Movies sorted by production year"
Where the different symlinks are pointing to the same movie.
Also, multiple parts like Band of Brothers etc get's easy to be organized as you like.
Here's a big one; would it be difficult to do a linux version of your soft?
I am guessing that you cannot be too far off, having it in both Win and Mac anyways, but then again, there may be obstacles... (there often is...