One of the most important parts of riding is the building of proper habits...
And using both brakes for every stop is one way of achieving this. When we use both brakes, not only are we creating good riding habits, but we are also learning what each brake is capable of. How much play is in the lever? How much pressure should be used for each individual stop? How is the application of each brake modified from leisurely stops to hard stops?
Knowing each brake inside and out is crucial when the city street starts throwing you the curve ball. For instance, the 70 mph-screaming in your helmet-I don't want to die-hard-stop calls for a perfect balance between a serious and progressive pull on the front lever and enough finesse to keep the front wheel from locking up. You're probably going to lock the rear wheel, which is ok as long as you don't release it. If the rear brake locks, the bike will feel a little squirrely. Don't allow this to take your attention off what is important: 1. the front brake 2. keeping your eyes locked solid on your escape route or the place with the most stopping room. Continuous practice of hard stops at different speeds will help you to get this right so it's there when you need it.
However, knowing the rear brake is equally important in other situations, such as driving off the road at speed. In the dirt, pumping the rear brake as you down shift seems to be the best approach. I've personally driven off the track at Jennings GP at turn one at over 100 mph twice, and this technique saved me from going down both times.
The type of bike you ride plays into this as well. If you ride a big cruiser you're going to get as much as 30% of total stopping ability from your rear brake. Practice will enable you to account for this during your stops. With sportbikes, however, your rear brake is more of a stabilizer during hard stops and should be used as such. Either way, keeping your eyes up and on your escape path is crucial. The harder you stop the harder it is to keep your eyes up. So practice!
Finally, don't forget your downshift. Getting stopped in time is only part of the battle. If that step van behind you can't get stopped (and he probably can't) you'll need to get out of his way. This won't happen if you're stopped in 4th gear or sitting in neutral.
So, use both brakes and downshift to 1st gear during all stops. And practice.