I really don't adjust mine too much from the systems you have listed. Generally speaking, here are my settings:
Output resolution: 720p (1080p has fucked up scanlines, 480p works well too if your TV can upscale it well)
Image Mode: Picture (for progressive sources, natural can be good too. Standard sometimes if a particular system is noisy)
Screen Set: Standard (Except SNES, due to not having square pixels it needs one of the other modes. Normal2 I think.)
Brightness 20
Gamma 10
Black 0 (I sometimes fool with Brightness and Gamma, I never touch Black)
Sharpness 1 (occasionally I will switch to 0, but never, ever higher)
Auto Scaler Off
H Scaler 6
V Scaler 5 (Note, you can fiddle with the scalers a bit to adjust sharpness. This generally works better than the actual sharpness setting)
V Width (leave at 32 except MVS needs to be changed to 33 for scanlines)
Scalines 80
A/D Level Somewhere around 140 for most systems, my CMVS has to be set to somewhere around 90 or 100 though.
I'm not saying that these are the best settings, but it's what I seem to find as the best combination with my plasma. I'm always open to suggestions though.