As with Dave's answer, it is preferable to breath in through your nose. Your nose has evolved over the years to do a great deal of filtration, from filtering pollutants to warming the air as it comes in to adjusting the humidity. Breathing out has been more debated with some people claiming that breathing out through the nose helps you keep from getting dehydrated (the moisture gets caught on the nose hair and mucous membranes so that it can hydrate incoming breath) and others claiming that breathing out through the mouth helps clear more CO2 from your system.
The one exception that I've run into, and it's a big one for some people, is whether you can get enough air through your nose. If you have a cold, or you suffer from allergies, it may be impossible for you to get sufficient oxygen through your nose, and the process of trying may make things worse (the nose is where the primary mechanism for respiratory allergies activating lies). So ultimately, if you don't have obstructed nasal breathing and you don't suffer from severe allergies, I recommend breathing in through the nose. When your nose stuffs up, or when you can't get in enough air to sustain your exercise, switch to mouth breathing as necessary. But hold off on the latter to train yourself to increase the amount of breath you get in through your nose rather than relying on mouth-breathing from the start.