I'm still a topclip user. Yup - I still have kerosene lamps and a cow out back, too. But I've notice FAR more knee problems among touring cyclists since clipless came into fashion. I'm no sports medicine doctor, but I suspect it has something to do with repetitive motion injury. Even with "floating" pedals it tends to place the stress on the same point. Perhaps for 90% of people, clipless is way better - but for that other 10% it can be a disaster. Toeclips allow you to constantly reposition your foot ever so slightly - the way your foot will automatically recoil from a sharp object, you may not even notice it. Yes, you'll have less "efficiency" but if your knees go you'll have ZERO efficiency.

Two suggestions - are you mashing potatoes - i.e. not riding in a low enough gear? Try riding in a gear one gear lower than previously. Otherwise, if the knees keep hurting, consider switching out to toeclip pedals. You can always keep both for a while and mail back the ones you decide against. Another nice thing about toeclips is that you can ride in your Tevas and your feet stay nice, cool, and dry - and they say "Thank you!"