The dent above your knee sounds like it is in the vastus medialis. This muscle has a pronounced bulge in bodybuilders and athletes with good powerful legs. It sounds like this is the area showing your dent. There are exercises you can do to build up this part of the muscle if it is just a muscle /exercise problem.
Atrophy is the wasting away and shrinking of the muscle. In my case, my left calf atrophied. There was no pain and I didn't even notice it until I lost the ability to do calf raises or stand on my toes on either foot. At that point the atrophy was visible and my PCP measured the loss at 1 inch.
As to the hand dents, TexasTracy's pictures shows pronounced atrophy in the FDI (First Dorsal Interosseus).
Tracy, do you also have significant atrophy in the APB (Abductor Pollicis Brevis) which is the muscle on the base of the thumb that joins the palm. That also leaves a "dent" that, I believe, ClearwaterAl, Mediasmart and I all share. Atrophy of the FDI and APB are being viewed as possible sign of the Split Hand which researchers in Australia, India and Canada (at least) are viewing as a definite sign of ALS (and almost no other disorders).