If you're looking for maximum crunching performance, you should look into dual socket motherboard with highest amount of cores per CPU within your budget.

Why build a super-expensive machine when you can build two (or more) simpler machines with the same money and probably get a better end result?

For example you can build a powerful cruncher around a good i5 or i7, with no fancy stuff, just the basics (modest hard drive, good PSU, enough memory), easily for way less than $1000. With less than $3000 you can build 3 of these! Even with a good GPU on each you'll spend less than $5000 and you'll end up with a farm more powerful than the Xeon-based alternatives you suggested (3x8=24 cores with i7, plus the GPUs).

I also agree,
Given the intended inclusion of a GPU project, if you buy a computer now, make sure it is able to support at least one big GPU.
The requirement is thus a big enough case to fit the GPU, and a PSU that is able to support at least one power hungry PSU. We have no idea of the points system wrt GPU's (or if there will even be one) but if a GPU can do 10 to 60times the work of a CPU for HCC then for many the balance will shift towards using GPU's, irrespective of credits or badges.
So if you are looking for a new system, or several, be sensible and get a descent high end system to which you can add GPU's, and don't go spending too much on dual socket server rigs. When you consider there could be 16thread single socket CPU's within 6months, it makes little sense to spend $5K on a new server rig now, especially considering the stated $3K budget!

I too agree...especially with the costs of gpu's going up and up and up and that you will do better with a matched set than two different ones. Two different ones WILL work but not like a mathed pair will! You can get some very nice dual pci-e slot mb's cheap, put in a nice i5 or i7, or AMD 6 core, add two gpu's, a hard drive(160gb will work) and 8gb of ram and you are good to go CHEAP!!! You will then be up and running on one machine and then turn your resources to a 2nd then even a 3rd machine as tme and money permit.

Oh and btw if you buy a 4tb hard drive system what the heck will you back it up to?!! If you really have that much stuff you NEED then you will need at least that much space to back it up to, if not TWICE as much!! That emasn you will then have to build yourself a backup machine which is even more money! My advice...keep it simple in the beginning and expand as you think this thru. And also remember the 1st rule of buying pc stuff...whatever you buy today, tomorrow something will come out that is even faster, better and cheaper!! Put all your eggs in one basket and you will be very happy for the short term, but upgrading later on is not a likely scenario! But something you can upgrade in pieces as that is usually how the money comes in.

FWIW I would wait on any dually setup until Intel releases SB-E and IB. There are 6 and 8 core HT chips coming. You may spend a little more on costs up front but the power savings will be well worth it and the computing power will far exceed anything that AMD has now or will have for the forseeable future.