Nylon seems to be the most popular skin. Good and tough but not a lot of coatings will stick to the nylon. So you are sort of limited there. Plus nylon is hygroscopic, meaning it absorbs water and when it does, it expands. That means it loosens and wrinkles on your boat. (yes, it does it even after it is waterproofed) Once it dries it goes back to drum tight. Some people have been able to get it tight enough it doesn't wrinkle, I have not been able too.

My experience is the 12 oz nylon is less prone to this and after a few paddles it seems to loosen up much less. To the point it doesn't wrinkle, just goes a little loose. The skin boat school has some good video's online showing how to sew nylon.

I prefer polyester fabric. It's not as stretchy as nylon so it is not as impact resistant, but I have never put a hole in polyester boat (I have nylon.) Polyester doesn't relax when wet and most any finish will stick to it. You can even use water based paint but I prefer oil based products, they are tougher. Polyester will also heat shrink so you sew the skin on a little loose and shrink it tight. The only polyesters I am aware of are a very loose weave and if you try to use the methods shown for nylon your going to end up with a royal mess.

So, I created a 3 part video showing my way of sewing on polyester.
http://kudzucraft.kudzupatch.com/video/skinning-polyester.php

Either one can make a excellent skin, it's just what you prefer and are comfortable with.