I've been on Starting Strength for 3 months, and although I initially gained some fat (due to not getting a lean enough source of protein) I've gained a lot of muscle. I feel much healthier, and like you my knee pain has dissappeared. Squats and deadlifts are awesome, and the overhead press is a highly underrated exercise. (I'm a big distance runner, and I think too much distance running over time atrophied all of my muscles, including my lower body muscles. The reduced strength at the expense of increased endurance made me more susceptible to knee injuries)
Edit: In response to those who claim squats are bad on the knees, let me clarify what a proper squat is: Depth. Believe it or not, if you only go to "shallow" depths in your squats, you put more stress on your knees than going "deep"(to a point where you're femur is slightly below parallel with the ground). This is simply physics at work. Stopping the squat at any point that is less than parallel is stressing the knees, rather than the much stronger hip flexors, which bear load in a deep squat.
Edit: In response to those who claim squats are bad on the knees, let me clarify what a proper squat is: Depth. Believe it or not, if you only go to "shallow" depths in your squats, you put more stress on your knees than going "deep"(to a point where you're femur is slightly below parallel with the ground). This is simply physics at work. Stopping the squat at any point that is less than parallel is stressing the knees, rather than the much stronger hip flexors, which bear load in a deep squat.