There are a lot of different opinions on how much front brake and how much back brake to use to bring your motorcycle to a safe stop, and a lot of that depends on the road surface and weather conditions at the time you're riding.
In general, a motorcycle gets most of it's stopping power from the front brake, between 70-85% in most circumstances. However, if you brake too hard with the front, you run the risk of locking the brake and flipping your motorcycle. Since this is annoying in the least, and deadly at most, let's look for some middle ground between the front and rear brakes.
In most stopping circumstances, you will be using a combination of both front and rear brakes to bring your motorcycle to a safe halt. If you're riding your motorcycle on side streets, chances are you're in the 20 mph range. When riding this slowly, your back brakes can provide most of your motorcycle's stopping power. As the motorcycle slows, you'll feel the weight transfer to the front of the bike. Now gently apply some front braking action and ease off the rear brake. This should give you a very smooth stop.
The situation changes at higher speeds. When stopping your motorcycle at over 25 mph, you will want to apply about 75% of your braking power with the front brake, and only about 25% with the rear. Again, as you feel that weight transfer to the front of the bike, easy up on the rear brakes and give the front brake more pressure.
The most important thing to remember about braking your motorcycle under any condition is that you should never apply your brakes so quickly that it causes them to lock up.