Personally, I try to organize in a way that makes sense and is relatively easy to read. To me, that would mean putting the simple options in some order (either by type or, more likely for me, in alphabetical order), then putting more complex items (such as your "all" option) lower (also ordered), with the "help" option (if present) at the end. (I would also probably have the help() sub close by, so it would be easy to remember to update if an option were added/removed/changed.) I might also consider storing those configuration options in a hash, so as to make passing them easier.

Hope that helps, and I look forward to the responses you get on this thread for the possibility of ideas to consider as well.