EPSXecutor rules!!! I don't even know how Pete created it considering that it goes way beyond command-line stuff. You can configure every game to run with the best game-specific plugins and settings. It would be sweet to have something like that in PJ64 so you don't have to switch between Jabo's/Azimer's/Glide64/Rice's, force normal blending, etc. Plus it's easy to forget that certain games work better with certain plugins (or settings) so then you have to figure out the best settings all over again.
PJ64 is great the way it is, but just like with ePSXe, it would be enhanced so much with a great frontend.