Buy a Goniometer (£6-£8) from a medical supply store - it's just a big protractor to measure knee angle.
Get yourself on your bike and measure the knee angle (from hip through to ankle bone)when at full pedal extension. That is pedal in line with seat tube NOT at the bottom of the stroke. I actually use a black dry wipe marker and draw a line through my joints (actually my wife does!) Then it's dead easy to measure the angle.
Shoot for about 25 degrees. I have found this to be perfect. You can go with a higher saddle height than this - like down to 15 degrees but like Matt said below I have found my seat height being a touch lower is better, so for me 25 degrees is the ticket.
Next step is to fine a loving wife to repeat above steps whith all your bikes so you know your critical measurement is exactly the same regardless of shoe type, pedal, crank length etc.
Never had any knee issues since I use this method.
Now, you will all think I'm sad no doubt but I also recorded my leg movement on video while on the turbo and that's something I'd recommend doing as you can really see the diffence it made. I kept adjusting until my foot was coming through the bottom of the pedal stroke parallel to the ground. That was most comfortable for me and It's how I came up with my 25 degree angle. Others may ride toe down etc but you can quicky feel the sweet spot and with the goniometer replicate it accurately on all bikes. remember though if you change things your body needs some time to adapt, so don't go and change it right before a race eh!
I need another hobby, I've turned into a right nerd............