I use Speedplay. They were easy to learn to use, both for me and a couple of my friends that I "sucked" into cycling. A previous post mentioned they have "float". In case you don't know what this means, it means you can move the heel of your foot in and out slightly. You are not locked into one specific place, which could potentially help with your knee issues.

On a side note, be very careful that your saddle is positioned properly, or you could have further knee problems.