+1 for Speedplay pedals, and you might also consider wearing a cho-pat strap on your knee for support, depending on what the problem is with your knee joint.

My orthopedist told me my kneecaps are ever so slightly turned outward, compared to most people's knees (lucky me ), and as a result I need my feet to sit at kind of a weird angle on the pedals to keep my knees from complaining (though only the left is really insistent about this). My LBS guy recommended Speedplay Frog pedals--they have about a million degrees of float, which is great for my whiney knees.

I also wear a cho-pat strap on my left knee for support. There's some controversy over whether this contraption is really effective, and maybe I'm a victim of placebo effect, but my knee seems to feel much better when I wear the thing.