For a stop sign or in traffic, I leave it in gear and clutch as needed. At a red light or another time where I'll sit for a bit, I kick it out of gear and let off the clutch. Leaving your hand on the knob could cause premature wear (over a very long time) on old external shift rail transmissions (Muncies, Top Loaders, T-10's, etc.) but does nothing on a modern transmission. Some cars require a certain gear when parked. The 2005 (only) Corvette (first year for that body style) had to be put in reverse before the car was turned off (also first year for the push to start) or else the battery would run down. I do not use reverse to park because reverse generally uses a safety of some sort. In a modern h-pattern manual, I use 2nd to park to have a higher gear ratio and because it's the easiest gear to pull.
And to be technical...vehicles are not built with emergency brakes. There's too much implication in that name for the manufacturers. It's generally called a park brake (and generally always has been). Most modern parking brakes would help zero in an emergency.
Slowing down: I use both. If I am slowing down enough, I will have to downshift to accelerate anyway. Once the shift is made I let the engine slow the car until the next downshift but it all depends how much you're slowing down and how much time you have to do so. Downshifting doesn't wear the clutch any more than upshifting. Starting from a stop is where most clutch wear comes from.