Hey, so FRED's been bugging me since like... forever.
I want to lock my fighter's weapons, naturally I look for lock-primary-weapons in the... subsystem menu.
And I want to set a death message. Why that's in Special, because the messages menu thinks that sexp smells funny.
Well, NO MORE.
Equipped with a version of Visual Studio that can compile FRED, I dove in and fixed this silly organizational nightmare to the best of my ability! Now things make slightly more sense than before!

ship- sexps in Ship Status! Subsys- sexps in Subsystems! It's a miracle!
Generally how its laid out now is ship related categories, then mission related, then back-end related (variables). Within each subcategory, the sexps are grouped the best I could to their function. Protect sexps are bunched together, lock weapons are grouped together and so on.
http://pastebin.com/0bqcJWEaHere's a patch of my work. If you have a better organizational method, I'd love to hear it!
(Aaaaaand cue the "But I'm so used to old way" comments!)