Almost no one really understands throughput and how to achieve it.
Most people focus on MHz because that is an easy to understand number.
Let's go down your list Jesse and see where improvements can be made. I'll be assuming that we are limiting our choices to a 'Wintel' machine. P3 is good, but since money is no object I'd get a P3 Xeon. The L2 cache runs at full processor speed instead of half like the P3. Since we will be running NT exclusively and not 9x, we will be running two processors.