Recently I've been riding longer and longer distances (100km+) and I've noticed that the next day it's sore behind my knee caps. Is this posture, seat position or just my body getting used to the work?
Live life one century at a time.
What xerxes says is true. When this happens you can develop a condition called chondromalaica patella, a roughening of the cartilage that lines the back of you kneecap. The quads becoming out of balance through cycling can be a cause of this, or a partial cause of it. Other things like using pedals/cleats that are aligned properly or have no float can also be the cause. Also, a saddle position that is too low can cause it.
Make sure your cleats are aligned properly, your saddle is positioned properly, and then start doing daily isometric exercises called "quad sets". Also, a good rule is to not increase your mileage more than 10% from the previous week.
You may have your seat too high causing you to overextend when peddling.