There is nothing I hate more with HDR photography than Shadow Noise and Highlight blowouts. These areas are especially common when tone mapping with Photomatix Pro. While they are very annoying, they are not worth throwing Photomatix out of my HDRsenal by any means. After taste testing many, if not all, of the HDR tone mapping software on the market, I find Photomatix to be the best. You cannot beat that look that is created with Photomatix, many other tone mapping products make the HDR images look milky and high contrast. Not Photomatix!
So how do you deal with the Shadow Noise and the Highlight Blowouts in Post? The short answer, for shadow noise, use the Dust and Scratches Filter in Photoshop. For highlight blowouts, use the Patch Tool. If you need more description or would like to see how I handle them, check out this quick tutorial.