BizHawk is a multi-system emulator written in C#. BizHawk provides nice features for casual gamers such as full screen, and joypad support in addition to full rerecording and debugging tools for all system cores.
-No info on the control bytes, so I'm not dealing with them right now.
-It seems like there's an extra byte for at the beginning of input for NES that doesn't exist for PCE.
--I think it might be the "1 byte for power-on and reset" that the docs refer to, though I'm not sure why this would exist for NES and not PCE...because NES supports control commands and PCE doesn't?
--Perhaps this will become more apparent if I write the importers for SMS, GG, GB, and GBA. I'll need access to a Linux machine to do these, though.