Years ago when I was learning to ride motorcycles I was told to apply the rear brakes hard first and then follow with the front brakes. The reason is by applying the rear brake hard, you squat the rear end. Now you apply the front also- the whole bike squats down and you have a well controlled two wheel braking. If you apply front brake first the front will squat and the rear will rise, and you are on your way to an endo.
On a bike with no suspension, the effect is far less pronounced, but I still find it beneficial to brake the rear hard first, and then follow a split second later with the front. As Cyccocommute says- it you over-rely on the front, you will find yourself lifting the rear tire.