I have made for you the Karnov Inspector! It's a Lua script that you can use with FCEUX, Bizhawk, or Mesen.

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Download: https://gist.github.com/bbbradsmith/46e53f67f681814337001445539995ad

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H - Help - Toggles the help display. S - Stats - Your screen coordinates, scrolling, and map coordinaes at the bottom. K - Tiles - All the level tiles: collision, hidden item triggers, spawn triggers, etc. L - Touch Hitbox - All the hitboxes that you can touch. V - Shoot Hitbox - All the hitboxes that you can shoot, plus enemy health. B - Bomb Triggers - All the places you can use a bomb. N - Hide Screen - Blanks the image to view only the inspector overlays.

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This should work with most versions of FCEUX, but I recommend the "interim" build available here, which will display the overlaid colours a little better:

http://www.fceux.com/web/download.html

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To run this, open Karnov in FCEUX then go to: File > Lua > New Lua Script Window > Browse...

I now consider this complete with version 1.0 being released. I have amended the initial post with all the details. I don't plan any further additions, but let me know if there's something I've missed, or if you have any comments at all, really. Enjoy!

@rainwarrior

I've done some search & replace'ing to make Karnov Inspector work on Mesen 2.1.1. Is it ok with you if I post it here?

Sure, I could also add it to the original gist with attribution to you if you like.

I feel silly now, because I just realized the only thing that needed replacing was the memory read function.

from (Mesen 1)

function memory_readbyte(a)
    return emu.read(a,emu.memType.cpu)
end

to (Mesen 2)

function memory_readbyte(a)
	return emu.read(a,emu.memType.nesMemory)
end

Ah, that's great. I'll just update the gist with a comment then. Thanks for your help!