- The bookmarks you create inside a media file (using the bookmark tool) should be stored in a "bookmark file" (for example in the VLC application directory) to remember the bookmarks even after you close VLC.
- The bookmarks should be assigned to the file based on the media file extension + the file size + media caracteristics (video resolution, codecs used etc...) + approximate file name (so when you rename the file (add the name of the film maker, remove the dots, etc) the bookmarks will still be related to the good file) but not based on the path where the media file is stored (so when you move it, burn it etc the bookmarks will not be lost).
We could also think of a way to recognise the video independently to it's filename by storing in the "bookmark file" a couple of bytes taken from the media file (from the middle of the media file for example, from the middle+the end, or from any other offset combination in the media file that avoids the common headers that would make many files look the same).