Found it

MetalNES, transistor level NES emulation https://github.com/iaddis/metalnes

While searching I also found a new one, VisualNES https://kaiokendev.github.io/nes/about

There is also one for GB https://github.com/aappleby/MetroBoy

See also Higan, formerly BSNES, which among other things is a cycle-accurate emulation of the SNES hardware and its enhancement chips (like the SuperFX used in StarFox/StarWing):

https://en.wikipedia.org/wiki/Higan_(emulator)

RIP Near