I choose the standard ATX size so that in the future I could easily upgrade the graphics by putting it in SLI. Do workstation GPUs benefit from SLI as well as gaming rigs do? If not, would it be better to just use micro ATX?
How is he set for monitors? Does he like like the multi-monitor setups?
Has he been able to give you any guidance if the NV Quadro or ATI FirePro work best for him? And what series works best with his software?
microATX or mid-tower ATX is a personal choice based on what space is available. No limitations (or personal style preferences)? ATX offers more future upgrade options since a case has no problem moving forward into a new build. Match CPU cooler to size of case as well.
I like the i7-2600k not only for it's current stellar performance but also because it can take the next gen Ivy Bridge CPUs. No expected upgrade path for the 1366 X-58 i7/i9s.
Maybe bump that SSD up to the 90/100/120GB version or what ever the budget can handle.
Also match the workstation graphics card to the budget and software.