Which Brake Which Side?

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. A moment of confusion in an emergency situation can be deadly. The left lever on a motorcycle operates the clutch, which will not stop you!
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 European Union has adopted this as a standard, even though only the United Kingdom and Ireland are left-side driving countries. The standard is not universally observed; a reader has written in to say that the left lever usually controls the front brake in Denmark.
The theory that seems most probable to me is that the 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.

On the other hand, if you have already developed a preference, it is usually best to stick with it -- or at least, choose a few weeks of riding under undemanding conditions to retrain your reflexes. In an emergency, you must act faster than you can think. If you switch between a Mac and a Windows PC, where the same keys don't make the same characters, or between a clarinet and a saxophone where they don't make the same musical notes, you know how reflexes can trip you up. If you are used to skidding the rear wheel with the rear brake, switching the brake cables can result a flight over the handlebars. If you mostly use the front brake, switching the cables can result in rear-wheel skidding and increased stopping distance. These problems are most likely when first riding an unfamiliar bike, so, again, always test the brakes with a light brake application when you first start out.

See also my letter to Bike Culture magazine.