This may sound random, but what the hell. A suggestion that popped into my head the other day.
The PJ64 ROM list (the main columns/rows screen) reminds me of in MS Windows when you choose "View list" for the icons. You know what "View thumbnails" does right? - so I was thinking if a choice like that was implemented into PJ64, so when selecting your game it would show you box-art for the whole contents of your list, making the selection more... 'pictural'.
Not essential, will probably be frowned upon, but I thought it might be fun option haha.