Is going clipless shagging my knees?

It may be down to finding a system that allows your foot to move around more freely and find it's own natural angle/position. I find Eggbeaters good for that, whereas other pedals gave me a feeling my foot was trapped into position too much.

+1, i had the same problem with Aliums, but the Eggybeaters let me float like a butterfly.
i hear speedplays allow this kind of 'slippery' feel as well.