Actually, the President was just adhering to an obscure Washington tradition. The practice of using multiple pens to sign important legislation dates at least as far back as Franklin Roosevelt. The rationale is fairly simple. The pen used to sign historic legislation itself becomes a historical artifact. The more pens a President uses, the more thank-you gifts he can offer to those who helped create that piece of history. The White House often engraves the pens, which are then given as keepsakes to key proponents or supporters of the newly signed legislation.
When Lyndon Johnson signed the Civil Rights Act in 1964, he reportedly used more than 75 pens and gave one of the first ones to Martin Luther King Jr.
Once they're given away, some pens wind up in museums; others are displayed proudly in recipients' offices or homes. But they sometimes pop up again, like in the 2008 presidential campaign, when John McCain vowed to use the same pen given to him by President Reagan to cut pork from the federal budget.
Not every President goes for the multipen signature, however. President George W. Bush preferred signing bills with only one pen and then offering several unused "gift" pens as souvenirs. Even a piece of legislation as famous as the Homeland Security Act got only one line of ink. When it was over, the President is rumored to have pocketed it.
Times Magazine for the explanation.
The White House page on Flickr for the photos.