Oh, this is a great post ! Here's my set-up :
AF+MF button for focus setttings (everything available under that one control, from focus size box to zone to location and center reset, love it). C1 is Peaking color as I'm primarily a live targets manual focuser, magnification is totally useless in my case, never used it. I found out it is available with the AF/MF button though when a manual lens is attached. C2 is AF modes (S, C, DMF...), C3 is DRO levels, bottom key the thumb wheel is Peaking level (hardly ever change it, but handy in case).
Fn menu goes : ISO (that doubles the rotating wheel function but goes between selected values faster), metering mode, , Creative Styles (Landscape +1 contrast, +1 sharpness), Picture Effects, image ratio, image quality. Bottom row of Fn menu : Flash mode, zebra (set to 95 as an experiment), audio levels display, Soft skin (set to Low I love the output !), Face detection, and Steady shot.
I also leave it on Airplane mode at all times to save battery life. Works peach.