JulianSidewind :
If you are doing scientific computing, I would like to point your attention at this. I don't know how intense of computing you need, but this is something good to be aware of.
http://www.tigerdirect.com/applications/SearchTools/item-details.asp?EdpNo=4259469&CatId=4044
Watch the video to fully understand. It amazed me when I saw it.
If you do end up using 1 or 2 of these cards, then it is your choice on which processor to use because a dual channel motherboard should be able to provide enough ram, but if you use 3 or more, may i suggest the intel because of the motherboards allowing triple channel ram allowing you to have more, as you need an extra 4Gb of ram for each of thee cards added. The video will cover this.
Indeed, a HPC graphics card is superior to a CPU in raw calculating power. Take a look at Nvidia's Tesla and ATI's FirePro lines, these are better in some cases.
But may I recommend the AMD Phenom II X6-1090T or X6-1055T? These are 6-core CPU's that outperform the Intel 930 and even 950/970 in threaded workloads (which as far as I know most scientific software pieces are). Massive processing power per dollar.
As for your question:
AMD 1090T/1055T:
+ Equally expensive with more cores, so more cores for the same budget
+ Higher performance per dollar
+ Motherboards are *excellent* in price to feature ratio
+ Better future upgrade paths
- Less calculating performance per core (although the difference is marginal compared to the advantage of extra cores)
- Motherboards can only use dual channel memory. Not a big disadvantage, but take it into account
Intel:
+ Higher performance per core
+ Triple channel memory
- Motherboards have features that are as good or even better than AMD's, but their price is so high they are absolutely inferior to AMD's chipsets.
- No new generation of 1366 CPU's.
So my ranking would be:
1) AMD 6-cores
2) AMD quad cores
3) Intel quad cores