Amber lenses are good for seeing contour in the water, shallow water. If you were going to fish the flats for bonefish, permit, tarpon, etc., you'd want the amber lenses because they show up the contrast really well. The grey lenses are used a lot by the offshore guys because they block a lot of light, but not as good for situations that require contrast. But ultimately it does come down to a personal preference. Whether you buy an expensive pair or not, such as Maui Jims - I like the Ocean Waves -- you can test the two different colors. But they can be expensive. Another good option for a very good price are the fly fisherman sunglasses. i think they retail for under $30 and are pretty popular. Pat Sheldon is the owner, he is a decent guy, their Web site is:
http://www.flyingfisherman.com/2002/home8.02.html.