Yoga and stretching. If you can't get to a yoga studio just remember to stretch everyday and lookup stretches for the problem areas.
For the shoulder, try stretching one arm horizontally across your chest while you hold that arm with your other arm. Also think about doing lower back and pectoral stretches. You muscles are all connected in someway and stretching those muscles too can relieve shoulder tension.
For knees...try doing stretches for your quads like holding your leg by bringing your foot up to your buttocks. Also try calf stretches and hamstring stretches. Those bring the best tension and pain out of my body. I also notice when I don't do them, my knee will hurt after awhle.