I have checked our sprite list, and due to the fact that colors naturally changed slightly over the years, a very large amount have had a shade change. However, some Pokemon did experience dramatic changes, some examples are Spinarak(purple to blue)and Ninetails(the tails weren't very blue at all).
Other Pokemon I noticed with large changes(If you want, I will edit this to say what the changes were):
Geodude(this guy changed a ton)
Basically, any Pokemon from Gen. 1 or 2 will have had a dramatic change, because, as I said, the coloring in the games has changed a lot over the years.
Pokemon from Gen. 3 onward will not have had quite so much of a color change.