Paus is correct, freezing doesn't affect the honey in any way, and different honey colors come from the different colored flower nectars. I have some dark honey coming in right now. It happens every June, and I just can't seem to nail down exactly what the source is. If you have VERY dark comb, it can affect the color and flavor of the honey a little bit, especially if you are crushing and straining like I do, but other than that, the difference between honeys is only due to the nectar source.