>>/4286/
really depends on the region of your knee where the pain occurs (inside or outside).
there all kinds of solutions, like readjusting your cleats position, saddle height, position and type (some berts would tell you to get a sqlab saddle, can you imagine?) and   q-factor. 
I had inner knee pain (the side facing the bike), so getting pedals with smaller q-factor solved it for me.