Glucosamine Sulfate helps too. But it's a bandaid treatment - it'll relieve pain and kill inflamation, but if bike fit and technique are off, things are going to go wrong.
Oh yeah, about technique. No one has mentioned it yet. I've heard that keeping a flat foot throughout the stroke results in less stress to the knees. Either way, that's the proper method that every coach will tell you to pedal, so do it. Avoiding hard backpedaling... yeah, riding a brake will help a lot too.
I find that the more of these things that are present, the more crucial proper fit is:
-brakeless
-high gearing (76+ GI)
-regular hill riding
-regularly doing long rides (above 20 miles)
Seat should be just high enough that you don't rock your hips but can still keep a flat foot throughout the stroke. If the knees ache really bad and you feel it just sitting down or walking, take atleast a week off the bike. I had to do exactly that a few weeks ago because I was messing around with my fit and not realizing that I was royally screwing things up.
Oh yeah, cleat position on clipless pedals is crucial.