Is there a way to change the color of the rats nest that PCBNew uses? Ideally I'd like to be able to set the color of a specified net; specifically the GND net.
No, that isn't implemented currently.
You can file a wishlist item in the bug tracker.
GND is usually routed by making a large plane over an entire layer, which will allow you to ignore it for the most part, and give you the best EMC performance because current return paths are as close as they can be, minimizing loop area.