It would be reasonably straightforward to sort the sound, prototype, and font lists alphabetically when they are displayed.
Is there a specific workflow that you're having trouble with?
For example, in my current project, I’m using a lot of sounds and prototypes. For the sounds especially, it is hard to identify what I’ve imported/used/can get rid of simply because I have to scroll up and down trying to find that particular filename.
This is mostly because I’m a fanatic and will re-edit sounds if they’re too loud or the loop isn’t quite right.. so even though I organize all my filenames before import, they still end up out of order if I delete/re-import a re-edited sound because they’re plopped back down to the bottom of the list. Does this make sense?