Knee pain can be caused by a seat being too low, too high, too far forward, or too far rearward. (I think too low and/or far forward are more likely.) According to Steve Hogg, for a few people, it can even be caused by the HANDLEBAR being too low!
Terraferma 650b, Mondonico SL and ELOS, Masi Gran Criterium, Trek 610, Breezer Liberty, Georgena Terry Classic
Some old news: If your knees hurt in the front, your seat is probably too low. If they hurt in the back it's too high. If your pelvis is rocking left-right, it's too high because you are stretching to engage the pedals. This also tends to make you slide forward off of the sit-bone support area, forcing your perineum to be abraded (chafed, rubbed raw, bloody).
Not universal rules, but useful if you're out on a ride with a wrench and want to make an adjustment to prevent your shorts from being bloody when you get home. Make the adjustment before you have to start cursing, and make each adjustment a small one. Adjust one thing at a time (i.e. height or tilt, not both). For tilt, think it terms of lifting or depressing the nose by 1 or 2 millimeters at a time. Carry a ruler if it will help you.