I posted on just this issue about two weeks ago:
http://www.cyclingforums.com/t48553.html
I've had knee problems with surgery in one knee. After going through various pedals, I found that Speedplays aggravated my knee pain. The pain didn't seem to come from pedaling action, but from the release. The large degree of float translates into a large release angle which caused me more pain. I've gone back to Time pedals and filed down the cleat to keep my release angles tolerable.
Over the years, I've also found that having my saddle too far back (as was recommended by various fitters) gave me more knee pain. Another source of knee pain for me was the saddle being too low.
As for crank length, I recently purchased a crank from Graeme Murray in South Africa that allows one to vary the crank from 150 to 185 mm. Theory puts me, depending on the formula, anywhere from 172.5 mm to 185 mm.
When too short, I got knee pain (it was like having the saddle too low). I seem to like 175 to 180 best. At 185, I had no extra knee pain, but felt more ankle discomfort after 30 mile rides. For me, an unexpected finding was that the longer crank settings made it much easier, and more stable, to pedal when out of the saddle.
Regards, Robert