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Core 2 Duo is simply a superior processor. There exists no situation where the Athlon 64 is better anymore. Prices have fallen enough that C2D is always a better choice. Don't bother with DDR3, it's not good price/performance yet. DDR2-800 is more than fast enough for a C2D; get DDR2-1000 if you really worry about overclocking headroom.
Intel's chipsets tend to be of better quality than NV/VIA/ATI, too.
Unless you plan on mostly crunching FFTs with vector SSE-2 code, or you have some other very specific workload, I suggest going with an AthlonXP or Athlon64. The AMD processors offer much better price/performance than their Intel counterparts. The sole exception is the Pentium-M, which is an excellent and efficient chip. However, the Pentium-M is (tragically for low power/noise enthusiasts) only available in notebooks.
CPU should be selected mostly by your budget. For the lowest cost and highest price/performance, the Athlon XP 'Barton' cores still excel. Of these, the mobile 2500+ chips are the best deal. They are multiplier unlocked and easily overclock to high speeds (2200-2300MHz at 1.65V is relatively common). Note that overclocking is not guaranteed and is a risk. However, it is not a very major one.
The Athlon64 chips offer the best high end performance. It is again best to buy according to price. The older Socket 734 processors are on the way out and should probably be avoided unless your workload really likes the 1MB cache offered on some models. The C0 steppings are better overclockers than the B-steppings. The newer Socket 939 processors have the advantage of dual channel ram and an upgrade path. Added bonuses for all A64s and Opterons are a 64-bit memory model for large memory machines and hardware support for a real non-executable page bit distinct from the writable bit. These nice instruction additions are only available on x86-64 operating systems, which right now only includes Linux and some of the other free unices (FreeBSD and NetBSD at the moment). Windows XP users can still enjoy excellent performance in 32-bit mode; the Athlon64 is still top in performance.
As a remark, the A64s are among the coolest running chips for the performance that they offer (only the Pentium M has similar or better power performance). Keep in mind that only certain motherboards will support "Cool and Quiet" (dynamic processor clock adjustment as a function of load). CnQ is really a very useful feature, so it is worth looking for a motherboard that will support it. The AXP has good thermal performance, particularly when underclocked. The disadvantage of the AXP is that it lacks any sort of thermal throttling or dynamic frequency adjustment potential.
The new Prescott P4s are dismally inefficient and will require either a loud fan, underclocking, or exotic cooling to run efficiently. Older Northwoods are only somewhat less efficient than an AXP. All P4s support thermal throttling, but none support dynamic frequency adjustment.
If anyone is upset that I've neglected non-x86 CPUs, it is because I focus on price/performance. x86 slaughters everything in this respect simply because the processors are so common.