Some good shoes to consider: Powerlifting shoes, Puma's (with the flat sole), Chucky T's baby, and wrestling shoes (my choice b/c I have about 10 pair). Basketball or Cross Training shoes aren't bad because thay have less of a heel than running shoes
Tennis shoes (or shoes with more of a heel) are bad because of the angle they put you in makes it tougher for proper form of triple extension. Triple extentsion is fancy schmancy way of explaining how the ankle, knees and hip joint move during a squat motion. Proper triple extension (a squat) is performed by sitting BACK with the hips. The knees should move very litte if not at all. I agree 100% with TCR1 that going deep on squats is the way to go. Scientific studies show that this does not cause knee problems. They key is the relationship of the knees and the toes. Your knees should NEVER go beyond your toes. This causes overextension of the patella tendon --- hence knee pain. So when you squat you should look something like this (but lower
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Hoyt Contender, Sur Loc, Limbdriver, Easton, and really bad aim