As long as you don't get any big drips, balance won't be too big of a deal. I painted my CPU fan, and haven't had any probs, but it is a fairly low RPM fan.
I did mine 2 colors, blades chrome, and casing green(to match case). If you do that:
First paint the blades, don't worry about masking for when you paint the blades. After blades are COMPLETELY Dry, mask them off and paint the rest. Have fun, painted fans add a real nice touch if you do them well.