Depending on the injury or limitation that's affecting your knees, static (or held) squats can sometimes make a good alternative to their full-range-of-motion counterparts.
How to do it: Stand with feet hip width, arms crossed over chest. Lower into squat, keeping chest lifted and knees behind toes. Hold for 30 to 60 seconds then stand back up. Repeat up to 3 times.
Also try: Stability-ball front squat, static lunge.
