Knee pain is the number one cycling injury. This problem is particularly common in cycle tourists for reasons you will see below.
There are several different types of knee pain but the most common problem is a "overall" pain behind the upper part of the knee cap. It is especially evident when carrying loaded panniers up a flight of stairs after a long ride.
Some possible causes:
Riding in too high a gear: This is the most common cause of "touring knee" as the weight of the panniers makes it difficult to spin at over 75 revolutions per minute (RPMs) up hill. Count your RPMs. You might consider upping them to 75-85 to see if it brings relief.
Saddle Height: When seated on your bike with the pedal at the bottom most point you should have about a 25 degree flex in your knee. A saddle height either too high and too low can cause pain.
Saddle Position: In addition to height the saddle can be positioned forward and backward. When seated with the pedal halfway to the bottom you should be able to drop a line from the tip of your knee through the ball of your foot.
Foot/Pedal Position: For those using traditional pedals it is best to have the ball of your foot on the pedal. If the foot strays too far forward on the pedal it can cause knee problems.
Crank Arm Length: Sometimes shortening the length of the crank arm helps to alleviate knee pains. I know this is no help to those of you are the road in the middle of a tour.
Leg Length Differences: Are your legs different length? Have you set your seat height to the shorter or longer leg? Splitting the difference between the two leg lengths may help.
Cleat Position: If you are using a fixed cleat pedal, the cleat position may be wrong. Are your toes turned in toward the cranks? Are they turned outward? You may need to see how your feet naturally fall and adjust your cleats accordingly.
Cold Weather: Cover your knees. It really helps to keep them spinning happily!
Bike Fit: As you probably know, we are really cheap. A professional bike fit costs quite a lot of money where we live. Of course, the pros argue (rightly) that a well fit bike will save you in grief and injury in the long run. It is possible to do a good bike fit in your garage with the help of a friend or patient spouse. There are several good online resources, google "bike fit".