Cpu. xeon or i7 for work station? ecc or non ecc-ram

I'd go with a workstation board and ECC RAM rather than the gamer board and overclocker RAM that you listed. Get some Kingston unbuffered ECC DDR3-1333 RAM and a board that will support ECC RAM (a TYAN or Supermicro board, or one of the ASUS P6T WS series). Ideally you would like to have a dual CPU setup since some of those programs will take advantage of many cores, but you're not going to be able to do that with Xeons as decent dual-CPU Xeons (E5620 and better) start at about $400 and go up from there. You could probably get a dual Opteron 4180 system within your budget though, as the 4180s cost about $200 each and that would give you 12 2.6 GHz cores. The clock speed would be less than the W3565 but you have three times the cores and I bet it would be faster for your overall.