There's only two debugging emulators worth mentioning. Geiger's SNES9x and bsnes.
I personally use Geiger's because it's what I've been using for years. I haven't checked out the bsnes debugger yet.
~DS
Well I tried Geiger's and got "The application failed to start because the configuration is incorrect" or something, not sure what that's about. But I'll try the bsnes one.