E.g. a regular linear sort - alphabetical, breadth or depth first, etc. - is okay for the "leftovers", but I have an explicit priority ordering of things I want to see at the head of the list.
More advanced, what I did for automatically deducing a print order in the Cp/PL wikified manual / specifications:
- Create a manual table of contents
- Attach unlinked items to where first linked to, alphabetically ordered.