gray is when they are neutral such as if I were to give you rep it would be gray and wouldn't have much if any effect on your rep. The two shades of green are based on how much rep you get. They are based on a numerical amount such as if you had 2,000 rep points, then you would have a bunch of green blocks. They turn light green when you go beyond a certain amount or something.
Come on silly member since 2006 and you have never seen this Reputation FAQ You must have past that at some point, Oh like when you created this thread All the answers are in there Hope this helps