The components are all the same, except for the motherboard and CPU. One is the i7-3770K, an Ivy Bridge processor; the other is the i7-3820, a Sandy Bridge-E processor.
A few components are missing (power supply, storage HD, video card) because I plan on salvaging them from existing boxes. I have two GTX 480's and a GTX 470 that I plan to install, but in the future we might upgrade them to GTX 680 or whatever comes out in the future.
My application is scientific computing. I need this box to do two things mainly:
1) Rapid execution of single-threaded processes on the CPU 2) High bandwidth and low latency for communication between the CPU and GPU
From what I've heard, the i7-3770K (Ivy Bridge) has the following advantages:
3) Supports USB 3.0 whereas Sandy Bridge-E does not? This isn't a primary requirement, but since this is a workstation, rapid data transfer to external drives is a big plus.
4) Smaller transistors are "cooler"
The i7-3280 (Sandy Bridge-E) has the following advantages:
1) More memory bandwidth (quad channel, vs. dual channel for Ivy Bridge)
2) More PCI-E lanes for greater GPU/CPU communication bandwidth (40 lanes, vs. 16 for Ivy Bridge)
I'm leaning towards the Sandy Bridge-E processor because of the greater bandwidth. Some people say I don't need 40 PCI-E lanes with two GTX 480 cards - however, scientific computing applications can require very high data throughput (I don't know how to measure exactly how high) and it would be great to have a machine where bandwidth is not an issue. I think this is potentially more important than the performance boost on single thread execution that I'd get from the Ivy Bridge.
Overclocking is a minor concern. I've never overclocked any CPU (even though I've assembled 20+ boxes over the years), and when it comes to work-related hardware I am relatively risk-averse. That said, if one of the CPU can be more easily overclocked by a minor amount, it might affect my decision.