Pretty simple.

You can clutch and break from speed to a stop every time and you more than likely aren't going to wear out anything in the clutch in the time you own the bike. You will go through brake pads a little quicker than if you use engine braking, but then brake pads are cheap and easy to replace. Really, this shouldn't be a point of major concern.

If you take this approach, my only safety advice is that as you have the clutch lever pulled in and are braking, downshift through the gears as you are slowing down such that you are always in a gear that is appropriate for your speed. This ensures that if all of a sudden you need power to make an emergency maneuver, you will be in the right gear.

The alternative approach is engine braking, where you downshift through the gears with power to the rear wheel. Engine braking puts additional stress on your engine internals, but if you do it safely and with moderation, not necessarily any more than you will put on accelerating.

When I need to stop relatively quickly, and I don't mean just an emergency, I clutch and brake while shifting down through the gears. But if I'm slowly rolling up to a stop sign, or slowing up coming off of an off ramp, and there aren't any impatient drivers riding my tail, I'll slowly take off the speed with the engine down a couple gears, then clutch and brake while shifting down through the rest. Pretty standard.

 

I'd STRONGLY recommend against developing this habit.
If I understand the explanation given by biz44 here, he keeps his bike in N at red lights.
That goes against the recommendation of keeping your bike in gear while at stops.
In case you need to get going quick (you hear skidding brakes behind you) you'rebetter off already being in gear. I've heard the arguments about most people not really having the reflexes to get out of the rear-end collision from a stop even if you are in gear....but hell, I'd rather improve my chances by keeping the bike in 1st gear and the clutch lever pulled while at a red light.

 

Hot topic. I use engine braking coming off the highway, going down hills, etc. But when I am cruising the boulevard, I travel in the right gear and downshift as speed dictates. When stopping, I just roll up to the stop, downshifting with the clutch in at the appropriate speed should I have to accelerate suddenly, like when the light turns green, or making a turn left or right. I don't worry about wear and tear on the friction plates or the brake pads either. That's why they are made from wearable material to provide friction as warranted.