Note that what you seem to be referring to is an urban legend [1]. Initially both NASA and the Russians used pencils, but they were quickly deemed potentially hazardous because they shed graphite flakes that in microgravity may end up in places where you don't want them - being electrically conductive they may even cause short-circuits. Simple ball-point pens work fine in microgravity because they rely on the capillary effect, not gravity, to work.
Also, not mentioned in the Snopes article, is that the refill cartridge and ink used in the pen weren't even developed specifically with NASA in mind. Fisher wanted to create a ballpoint pen that would work in all manner of extreme environments, write on wet surfaces, and work upside down. Microgravity was just one of those extreme environments.
[1] http://www.snopes.com/business/genius/spacepen.asp