So this problem used to be rather "simple". Just use some CPU metric (MPIS, FLOPS, SPECint, SPECfloat, whatever) and divide it by the cost of a computer. Then we had a clear choice: 2 CPUs per "1U" system. Now the choice has expanded to cores per chip and we have 2, 4, and even 8-way systems (AMD). You could build a rack of Sunx6400, each containing 64 cores. But we also shouldn't forget Sun's T1 processor line, with 128 "virtual" cores.

Further complicating the issue: cost is no longer just for the compute node. Now you have to consider the networking costs between them. 100 Mbit Ethernet switches are cheap, but may not be suitable for a cluster of very fast machines. Infiniband gives you great performance, but scaling is very expensive -- just the cabling alone can cost as much as your CPUs!

Further complications: the operating costs of cooling and electricity are not insignificant. For every watt used by the CPU, you can count on needing 2 watts to cool it (depends on the climate you're in). Thus, if every computer node requires 1.5 A, and you have 256 compute nodes, you will need 1.5 * 256 * 3 = 1152 Amps of power and maybe 2 30-ton chillers.