Sit at my desk in front of my computer, if possible. Counters are too short. (A towel or two around on the desk for protection, though mess still occurs.)
I think many makers in Japan sit too, although that set-up where there's a pool of mystery liquid at floor-level and a bridge overtop, and you sit on the floor, doesn't look the most comfortable. Maxim's traditional sword sharpening imitation set up, which VB mentioned, looks better though I think the oval-ish wooden tub that's used is too small.
I think some kind of desk set up is underrated. At some point, some wealthy dude is going to come up with a custom table-level sharpening counter with sink, running water, stone storage shelves and tubs, or something.
A thought: if seated and sharpening at a height where your forearms are fairly level and parallel to the stone, wouldn't that give you the best control? The alternative would be your forearms come down at an angle, with each motioned you'd have to adjust, and that must be less consistent though many obviously get used to it.