Color. Most pictures won't show it, but the ms-3 is a very dark green and has a negative display, whereas the ms-1 has a black band and positive display. As can be seen below.
http://www.casio-intl.com/wat/watch_detail/?m=GD-100MS-3&n=675
The number designations on a g-shock will typically refer to band color and the letters with that number will be the country code. So GD100MS-1DR, the 1 refers to the color black, and the DR to American, ER for Europe etc. Common colors I've seen are 7 for white, 4 red/orange, and 2 for blue.