Since your bike has two brakes, one for each hand, if you want to stop as safely as possible, you need to pay attention to how you use each of them.

Conventional wisdom says to use both brakes at the same time. This is probably good advice for beginners, who have not yet learned to use their brakes skillfully, but if you don't graduate past this stage, you will never be able to stop as short safely as a cyclist who has learned to use the front brake by itself.

The fastest that you can stop any bike of normal wheelbase is to apply the front brake so hard that the rear wheel is just about to lift off the ground. In this situation, the rear brake cannot contribute to stopping power, since it has no traction.

The rear brake is O.K. for situations where traction is poor, or for when your front tire blows, but for stopping on dry pavement, the front brake all by itself provides the maximum stopping power, both in theory and in practice. If you take the time to learn to use the front brake correctly, you will be a safer cyclist.
Many cyclists shy away from using the front brake, due to fear of flying over the handlebars. This does happen, but mainly to people who have not learned to modulate the front brake.
The cyclist who relies on the rear brake for general stopping can get by until an emergency arises, and, in a panic, he or she grabs the unfamiliar front brake as well as the rear, for extra stopping power. This can cause the classic "over the bars" crash.
Jobst Brandt has a quite plausible theory that the typical "over-the-bars" crash is caused, not so much by braking too hard, but by braking hard without using the rider's arms to brace against the deceleration: The bike stops, the rider keeps going until the rider's thighs bump into the handlebars, and the bike, which is no longer supporting the weight of the rider, flips.
This cannot happen when you are using only the rear brake, because as soon as the rear wheel starts to lift, there is not more braking force generated by it. Unfortunately, though, it takes twice as long to stop with the rear brake alone as with the front brake alone, so reliance on the rear brake is unsafe for cyclists who ever go fast. It is important to use your arms to brace yourself securely during hard braking, to prevent this. Indeed, good technique involves moving back on your saddle as far as you can comfortably go, to keep the center of gravity as far back as possible. This applies whether you are using the front, rear or both brakes. Using both brakes together can cause "fishtailing." If the rear wheel skids while braking force is also being applied to the front, the rear of the bike will tend to swing past the front, since the front is applying a greater decelerating force than the rear. Once the rear tire starts to skid, it can move sideways as easily as forward.
If you don't believe me, perhaps John Forester can convince you...see his Entry in the rec.bicycles FAQ on Front Brake Usage. (Unfortunately, the maintainer of that site has a habit of breaking links, so you may need to go to the rec.bicycles FAQ index to find the article.)

Maximum braking occurs when the front brake is applied so hard that the rear wheel is just about to lift off. At that point, the slightest amount of rear brake will cause the rear wheel to skid. If you ride a conventional bike, the best way to master the use of your front brake is to practice in a parking lot or other safe space, applying both brakes at once, but putting most of the effort into the front brake. Keep pedaling as you brake, so that your legs will tell you immediately when the rear wheel starts to skid. Practice harder and harder stops until this happens, so that you will learn the feel of stopping fast, on the edge of rear-wheel liftoff.
Some cyclists like to ride a fixed-gear bicycle, that is, a bicycle that does not permit coasting. When you brake hard with the front brake on a fixed gear, the drivetrain gives you excellent feedback about the traction situation at the rear wheel. (This is one of the reasons that fixed gears are favored for winter riding.)
If you ride a fixed gear with only a front brake, your legs will tell you exactly when you are at the maximum brake capacity of the front brake. Once your fixed gear has taught you this, you will be able to stop any bicycle better, using the front brake alone.
If you find the fixed-gear concept intriguing, I have a major article on Fixed Gears for Road Use on this site, and also a page of Fixed-Gear Testimonials from happy converts.

Skilled cyclists use the front brake alone probably 95% of the time, but there are instances when the rear brake is preferred:

• Slippery surfaces. On good, dry pavement, it is generally impossible to skid the front wheel by braking. On slippery surfaces, however it is possible to do so. It is nearly impossible to recover from a front wheel skid, so if there is a high risk of skidding, you're better off controlling your speed with the rear brake.
• Bumpy surfaces. On rough surfaces, your wheels may actually bounce up into the air. If there is a chance of this, don't use the front brake. If you apply the front brake while the wheel is airborne, it will stop, and coming down on a stopped front wheel is a Very Bad Thing.
• Front flat. If you have tire blowout or a sudden flat on the front wheel, you should use the rear brake alone to bring yourself to a safe stop. Braking a wheel that has a deflated tire can cause the tire to come off the rim, and is likely to cause a crash.
• Broken cable...or other failure of the front brake.
• Long mountain descents, when your front brake hand may get tired, or you may be at risk of overheating a rim and blowing a tire. For this situation, it is best to alternate between the front and rear brake, but not to use them both at once.

Generally I advise against using both brakes at the same time. There are exceptions, however:

• If the front brake is not sufficiently powerful to lift the rear wheel, the rear brake can help, but the best thing to do is to repair the front brake.Typical rim brakes lose a great deal of their effectiveness in rainy conditions, so using them both together can reduce stopping distances.
  
• Long or Low bicycles, such as tandems and long-wheelbase recumbents have their front braking limited by the possiblity of skidding the front wheel, since their geometry prevents lifting the rear wheel. Such bikes can stop shortest when both brakes are applied. Tandem caution: when riding a tandem solo (no stoker on board) the rear brake becomes virtually useless due to lack of traction. The risk of fishtailing is particularly high if a solo tandem rider uses both brakes at once. This also applies to a lesser extent if the stoker is a small child.

There is considerable disagreement as to which brake should be connected to which lever:

• Some cyclists say it is best to have the stronger right hand (presuming a right-handed cyclist) operate the rear brake.
• Motorcycles always have the right hand control the front brake, so cyclists who are also motorcyclists often prefer this setup.

There are also observable national trends:

• In countries where vehicles drive on the right, it is common to set the brakes up so that the front brake is operated by the left lever.
• In countries where vehicles drive on the left, it is common to set the brakes up so that the front brake is operated by the right lever.

The theory that seems most probable to me is that these national standards arose from a concern that the cyclist be able to make hand signals, and still be able to reach the primary brake. This logical idea is, unfortunately, accompanied by the incorrect premise that the rear brake is the primary brake. For this reason, I set my own bikes up so that the right hand controls the front brake, which is not the norm in the U.S.
I also do this because I'm right handed, and wish to have my more skillful hand operate the more critical brake.
See also my letter to Bike Culture magazine.