I've recieved money with stamps from 2004, supporting Kerry and Kucinich.
It's absolutely NOT illegal. Defacement, rendering currency unfit for circulation, is illegal. Writing in the margins of a bill, so long as profanity is avoided, is not considered defacement. Similarly, a stamp or two is not considered defacement either.. so long as no security features (portrait, security strip, series, serial, watermarks) are obscured.
Wheresgeorge has only had one instance where the govt has come knocking, and that was in the site's early days when the owner was selling wheresgeorge.com stamps on the site. He was told by the secret service that he could not sell the stamps, since it would be like he was using currency to promote his for-profit business. As long as National doesn't sell stamps advertising ronpaul2008.com, there won't be any trouble from the govt.
However, I don't think it's the best way to get the word out. Many people who come across the bill will "think" it has been defaced, and they will associate Ron Paul with something that they believe to be a crime.
I have a link to ronpaul2008.com in my wheresgeorge bill notes though, so that anyone who enters one of my bills will see the RP message/link.