Geiger's SNES9X will trace as you execute if you tell it to. You may want to enable the "Trace Once" checkbox and disable the "Squelch" checkbox. The former will only dump the code once, which you can then sort using a console sort command to get a properly-ordered log. (If it's disabled, you'll end up with dozens of megs of logs for only a few seconds' worth of tracing.) The latter disables some rather useful output in the log if it's checked.