NES programs supporting Super NES controllerAlmost all NES games should work, from both the original and homebrew eras. They see B and Y on the controller as A and B. But the only NES program I know of that's aware of the A, X, L, and R buttons is my
spadtest tech demo.
NES programs supporting Super NES MouseThese include the Meece tech demo, Thwaite, Action 53 menu, Sliding Blaster, and the Sound Effects Editor remake.
How to build an adapterYou can plug the controller as is into an FC Twin famiclone, as
demonstrated in AWal's video. Or if you know how to splice and solder wires, you can build an adapter as described in
Controller port pinout.