If there's ONE useful thing my old, over-priced physio doctor taught me, it's to be damn careful about covering your knees (and elbows) in anything less than warm weather. I used to run 10k+ everyday, no matter what. I was one of those crazy people you see running in two feet of snow. That is, until my knees basically stopped working. My physio doc showed me a video of an athlete training in cold weather with temp readings all over his body. While his muscles stayed above 37*, his joints got as low as 22*, which is very dangerous, because they're isolated from all the warm blood and not shielded from the elements, esp. wind. Cycling really uses your knees, and if they're cold and stiff you can easily build up scar tissue around your knee, which is very difficult to break down. If you let it build up enough, eventually the muscles attached to the knee joints will not function properly, until you're unable to get up a flight of stairs pain-free unless you literally crawl (I am not exaggerating here).

Cover your knees with insulated, WIND-PROOF covers! Even under normal pants or tights.