Brushing at night is the most important. Saliva naturally fights the growth of bacteria on your teeth. Your mouth dries out at night and reduces your mouth's ability to do this. Ideally, you would keep your teeth clean at all times but that's of course not realistic. A while back I read many websites and opinions about this very question. The main consensus seemed to be that people brush in the morning because it makes them feel good to start their day with a clean mouth (not because it's the best time to do it).
Here is a discussion about it on Ask MetaFilter:
During the day, you're flapping your jaw, drinking water, chewing gum, and moving your tongue, all of which help to clean things off of your teeth. At night, your mouth is much less active, which allows bacteria more time to grow without being mechanically sloughed off.
Many years ago my orthodontist told me that it was most important to brush your teeth before going to sleep (I guess either for the night, or for a nap). Saliva production is down, and if you happen to sleep with your mouth gaping open, your teeth dry out and don't have that protective layer of saliva. Just the lack of movement of your lips and tongue while sleeping gives decay more of an opportunity to do its dirty work.
Here is an article by Dr. H.S. Chawla:
Brushing before meals: Most people normally brush their teeth in the morning before breakfast. That is beneficial, as you have reduced the number of bacteria before exposing them to food. The amount of acid production is expected to be less, and so would be the damage to the teeth. You get an additional benefit if you use fluoride tooth paste, as the fluoride gets incorporated into the enamel and makes it strong and resistant to the effect of acid. (Fluoride converts the hydroxyl-apatite of enamel to calcium fluor-apatite).
If you are going to brush in the morning, it may actually be better to brush before you eat rather than after.
brushing right after eating is not at all advised, as the acid produced [by bacteria] has already begun the process of eroding enamel. If you brush promptly after a meal, you rub off part of the dissolved minerals of the enamel.