If the squat is troublesome for you, the best alternative exercises to consider are exercises that mimic either the joint action or muscle groups involved in the squat.
The squat is often referred to as "the king of the gym lifts"—for good reason, too. A correctly performed barbell squat utilizes virtually every muscle in the body.1 If you want to get stronger, squats will help. If you want to get bigger, squats will help. If you want to lose weight, squats will help. As such, most good programs will include the squat.