Well in my case it's RTAS and Pro-Tools does it for me.
But to be honest; I just remove anything I don't use on EVERY mix; so I don't have an enormous list of shit to scroll through to find something useful.
Organize? What is this I don't even
Joking aside, I just put them in folders if I really have to. Usually I just open the add new FX in Reaper and type the name, it's quicker for me I guess.