From memory there are two AF versions of the 300mm f/4, the AF and the AF-S. All AF-S lenses are D. I don't think Nikon made a 300mm f/4 AF-D, but I could be wrong.
The AF-S has better optics, much faster autofocus and focusses closer. The AF is still an alright lens.
D means that the lens gives the camera Distance information, it's inherent in all AF-S lenses and all G lenses as far as I know. The camera uses it for better TTL flash metering and matrix metering. You don't need the feature, but it helps because the camera knows how far away your subject is and has a better idea of what you're using the flash to light.