I eventually worked out that my knee pain (only in the right knee) was caused partly by poorly adjusted, inward pointing cleats. Not only was I mashing, standing in the drops and pushing more than my weight, by pulling up on my bars, but I was also sort of locking my knees by pointing my toes inwards, causing my cleats to move to that position, forcing me to cycle toes-inward-pointingly.
When my knees hurt as they did yesterday, I do some upswing only rides with almost no push all pull on my cleats in imitation of Dr. John Bergman's first exercise of pulling knees and wobbling them. I must be pulling around 10kg. And I find that pull cycling works, especially (am I just imagining this?) if I eat glucosamine too.
When my knees burn I eat glucosamine and pull on my pedals using my cleats, and my knees seem to get better, until I mash in the drops again, or use poorly adjusted cleats.