I know a lot of people who use hair mascara or acrylic paint to color their eyebrows. I've tried a couple of ways to color mine, but I find coloring them white first with eyeliner, then applying the desired color of eye shadow has worked for the most accurate color.
Another way that I've colored my eyebrows has been with glue and eye shadow. You take something like an Elmer's glue stick, brush it over brows, and then apply the eye shadow.
Personally, I feel using eye makeup alone will make your eyebrows look more natural, but they can smear easily. Using glue or acrylic paint can keep them on longer, but it can make your brows harder to move if your's are thick.
Here's a thread you can check out if you want more ideas. http://www.cosplay.com/showthread.php?t=132030&page=3