Its not rocket science, just get the best crap you can. If the Os you will be using =32 bit, get 4gb RAM, if its 64 bit, get 8GB. AMD phenom 2 CPUs are prettymuch all around better then core2 quads, but not by a ridiculous amount. They cost more though. Whats the budget for this bad boy? If there's no budget, then get a freaking core i7.
I would also suggest getting a MoBo that supports DDr3. It really all depends on the budget though.