More than just duck hunt, I've also played hogans alley and trick shoot and just about as many of the zapper supported NES games that Wikipedia listed. They all worked just fine.
Oh, one thing to note is that FCEU doesn't put in zapper support automatically, you have to set the zapper as being active in your control setup option. The Zapper button is the Trigger, but you have to let GO of it for the shot to register.
The current SNES emulator also has Superscope and Mouse support that works, but I'm still figuring out everything to it. The mouse support has some issues though.
I finnaly managed to make it work!It seems that is necessary to activate Zapper support in port 2 instead of port 1.Anyway,thanks a lot!