The certification rules only apply to new stoves. There's even a tax break if you replace your stove this year, and it's been in place for the past two years. The EPA is exploring ways to help people change out their old wood stoves—those things are not healthy.
And that's about it. As one store page I found puts it: "When the EPA first started looking at woodstove particulate emissions, the front pages were emblazoned with headlines screaming, WOOD STOVES TO BE OUTLAWED!! When the regulations which specifically allow wood burning were subsequently passed, the story got maybe one paragraph on page 23."—The Chimney Sweep Online
Please, folks, stop posting scare stories. The Washington Times, where this piece of crankery comes from, is paid to scare you—by the Unification Church yet. So is Fox News. Just 'cause these guys want you scared doesn't mean you have to go along with the program.