Typical cycling newbie mistakes: Saddle too low, Gear too high ("mashing" rather than "spinning"). Since most folks guilty of these two things typically only ride their bikes around the neighborhood or campground, it doesn't matter so much. However, when riding for any distance (on a commute of 3+miles) these two things can conspire to cause unnecessary injuries.

As others have recommended, check out some bike fit websites to get a better idea of what to look for.

The quick rule of thumb:
1. Sit on the bike and have a friend stabilize the bike (handlebars or saddle).
2. Put your heels on the pedals and backpedal.
Your legs should be pretty straight at the bottom of each stroke (with the heels on the pedals). If your hips have to rock in order for the heels to remain in contact, the saddle is too high.

The proper positioning of the foot on the pedal is to have the ball of the foot over the axle of the pedal. The above method should result in a slightly bent leg at the bottom of each pedal stroke.