Full die capture, full transistor level simulation.
Most of the others are being emulated in proportion to their importance to games, in arcade machines and consoles. Those emulations are going to be as cycle-accurate as required.
There are some issues around things like the Yamaha synth chips, which are mixed-signal and depend on analogue properties that can be difficult to emulate.
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The 6502 is one of the most heavily preserved technologies: http://www.visual6502.org/JSSim/index.html
Full die capture, full transistor level simulation.
Most of the others are being emulated in proportion to their importance to games, in arcade machines and consoles. Those emulations are going to be as cycle-accurate as required.
There are some issues around things like the Yamaha synth chips, which are mixed-signal and depend on analogue properties that can be difficult to emulate.