Personally I would go for number 3. The Pentium D is the cut down, single core version so I would avoid that and all your getting for your extra $50 with number 2 is a bigger hard drive. You could use that extra and put a second drive in number 3. I am slightly biased in that I prefer AMD processors and ATI graphics, so that would swing it for me.
The specs are pretty similar, and some people don't like ATI graphics, I don't like Nvidia. If the price is important, you have a choice between 1 and 3, and there's no contest really. Just make sure you install Windows XP and not Vista to get the best out of whichever you choose.