It depends on the gear. I was using 52x16 ratio on a singlespeed for 2 months - no knee problems, and i ride hard.
Switch to a fixed sprocket today using the same ratio and my knees are hurting me.
It is very hard to not resist the pedal motion, even if you're not trying to brake with you legs, so it's harder on the knees. I think i prefer singlespeed.