I'm in physical therapy right now for my broken ankle and I asked my PT what the most common injury she sees is. Knees. She's says its because knee issues happen from young to old and for many reasons.
Knees are between two other important parts, hips and feet, so if you're experiencing knee pain, it's possible there is an imbalance somewhere else along the chain. One thing you might want to try is looking in a full length mirror. Wow, aren't you beautiful! And your legs are so strong! Anyway, about those knees. Do they bow out or are they knocked in? If you engage your quads to lift your kneecaps, do they lift straight up or towards one side? Do your knees and feet face straight ahead or in or out? Now look at your feet. Do you tend to roll to the inside or outside of the foot?
In a perfect world, we might all have exquisitely lifted arches with knees over ankles and everything facing forward. However, injury, imbalance, or simple range of normal variation in skeletons does not make this so. If your knees are knocked in, you might want to try strengthening the inside of the and legs and stretching the outside to bring balance, but don't necessarily force yourself into a prescribed alignment. Having an understanding of what your default posture is like will help inform you of imbalances and bad habits, but will also give you some idea of how to customize poses to prevent undo strain on your joints.
I've made a short video with a therapeutic, exploratory practice for knees. There's no weight bearing so there is minimal strain on the knees. This is a viniyoga inspired practice that will gently strengthen and stretch hamstrings, quads, abductors, adductors and all around the hips and low back.
Give the whole sequence a try and feel free to repeat, omit, or otherwise adapt the practice to serve you better. If you have an injury or imbalance, I recommend trying some of these poses asymmetrically, doing the right and left side alternately.
Stay tuned for part two for tips about stabilizing knees in more athletic styles of yoga!