Elmer's Carpenter's Wood Filler works great for me. http://www.redhillgeneralstore.com/A40266.htm
Thin with water to the consistency of ketchup before applying.
Much better than the latex based "lightweight" fillers.

This product reportedly works well for filling pinholes in fiberglass. (I haven't had a chance to try this yet)
http://www.darrolcady.com/Accessorie...nting_faq.html

I would not recommend using automotive spot putty on bare wood. (Dries too hard, toxic solvents)