I've modified the homebrew lacuncher to sort by folder name. I love open source. I'll send the code github, see if it can be added.
I'll try to make it sort by Title though, seems cleaner than folder name and a smdh editor has just popped out.
UPDATE: attached boot.3dsx that sorts per filename. It uses the latest source at github, so there should be no problems.
UPDATE2: been using it for a while and everything is fine (well, there should be no reason for it to not).
I'm working on multi-directory for hbl since it seems easy to add, I can get rid of my pseudo-folders