OK, so I have a program that is running a fullscreen window, set to be 640 by 480 pixels. Now, this is on my new vista powered notebook, and when I run the program with this window, instead of displaying it fullscreen at the desired resolution, its using the current resolution, and just displaying a small window of 640x480 in the center, with a giant black border around it. At first, it didnt bother me, but now Im just curious. Why does it do that? Im terribly new to this whole vista thing... and the notebook thing...

That's most likely a "feature" of your notebook. Look into the manual to find the key combo to switch between the scaling methods. On many notebooks it's Fn + F5.

Alternatively, find the scaling options in the display options of windows. I don't know where those are in Vista.