I went to see a physio about knee pain. She advised that my leg muscles were so stiff, and that all the muscles were so adhered to each other, that they were pulling on the patella. The result was a persistent knee pain whilst cycling and a dull ache for about 48 hours after a big ride.
I followed her advice, and now get a sports massage every fortnight. It's incredibly painful, and costs £30 a pop, but the knee pain has gone completely, and I never get sore legs, even when riding 400km or 600km audaxes.