Critique my academic/commerical build

I hate it. Really. You're basically throwing money away with that GPU. Non-gaming applications, especially those with heavy compuations, perform massively better with nVidia's CUDA features. ATI/AMD's cards don't offer anything along those lines. Even an older (i.e. non-DirectX 11 card) would be better than the 5750. I'd try to get a GTX 460 in there, but if it's out of budget, get the largest nVidia card you can afford. Something along the lines of the GTS 250 or 9800 GTX should cost about the same as the 5750.

I also highly recommend springing for the i7-870. The hyperthreading would be well worth the added cost (about $100). If you're near a Microcenter, you can find all Intel CPUs for a lot less than whay you can normally find. Of course, you can only buy from them in person, so if you're not near one, you're out of luck.

Instead of spending $80 on that case, I'd spend half that on the NZXT Gamma. It's a good case, and frees up some money else where.

I'm not a fan of the PSU. OCZ is rather low quality. There's a reason why they're so cheap. I'd try to get something from Antec, Corsair, Silverstone or SeaSonic. Look in the 450-550W range.

Unless you absolutely need the extra features of the Professional version of Windows, get the Home version. You'll save some money there.

I don't know the exact sticks of RAM you're looking at, but I'm guessing these Corsair 1600 mhz CAS Latency 9 are cheaper. You won't see a difference unless you're overclocking, in which case you'll need an aftermarket heatsink.

I also like the Asus P7P55D-E LX more than that Gigabyte board. The Asus has USB 3/SATA III support, making it more future proof. It's the same price (counting the $10 rebate).