I've read some posts on here about people claiming that having your seat too low gives people bad knees.

I think it's a myth. Yay or Nay?

It's true.

Saddle too low = front of knee pain
Saddle too high = back of knee pain

http://www.cptips.com/knee.htm

Not a myth.

Riding with your seat too low will leave your leg muscles screaming in pain. The lactic acid just doesn't get pulled away and absorbed by the body. Stick to correct seat height.

Knees definitely feel painful after a ride where the seat is too low. I've experienced it.

Seat too low and too far back causes much higher knee pains than too high or too far forward. Actually there's zero knee pain with too high & too far forward, it's really stretching the tendons & ligaments behind your knee.

Also too low a seat uses primarily the quads to drive the pedals and you end up overloading them. Having a higher seat allows you to recruit the hamstrings and glutes into the pedal stroke. You go a lot faster for the same effort.

Basic test of seat-height is to put your heels on the pedal and spin backwards. At the bottom of the pedal-stroke, you should have full leg extension. This is the lowest the seat should be and a lot of people have it 1/4 to1/2" higher depending upon the pedal-type and cleat-thickness.

Not a myth in my experience.

Does knee pain, secondary to improper seat height, also require the use of clipless pedal system for this to be true, or can it happen regardless of the pedals used?

Does knee pain, secondary to improper seat height, also require the use of clipless pedal system for this to be true, or can it happen regardless of the pedals used?

regardless. clipless can help make the pedal stroke smoother but knee pain can occur with or without them.

FWIW, saddle adjustment is critical (within a few milimeters) for me on my fixed gear bike, but not so much on my geared bikes.