Really bad fringing with nikon d5000?

Right, defringe should be done in RAW processing. That means when you open up your NEF file with PsE you should have a "Camera RAW" window pop up, in one of the sections for this, there should be a Tab for "Lens Corrections" In that you should have options for "Chromatic Abberation" in which there is a "Defringe" option.