I've always been told the angle of your knee should be between 25-30deg at the bottom of the stroke with your foot at your normal pedaling angle (do you point down, up or not at all).

Also, your knee should never go past your toes... In fact, with your pedals at 3 and 9 you should be able to drop a line (plumb bob) from your knee cap and it should bisect where the pedal axle is (or just behind)...never in front.

Also, also, if your seat is too low you'll probably cop some pretty severe pain in the front of your knees if you're doing some reasonable distances...