When faced with the same decision, I chose the D5000. I only have AF-S lenses, so the no in-body focus motor doesn't matter to me. If I want to control off-camera flashes, you can buy a commander unit and it's no biggie. The vari-angle lens and longer video recording sold me. I'd save the cash if I were you and get the D5000, or wait until Photokina and see what new bodies they release! The new D3100 might even be a good option for you.
