Parts Preferences: Intel CPU. Don't mind getting last generation cpu/motherboards. Micro-ATX MotherBoard
SLI or Crossfire: No
Monitor Resolution: dual 1680x1050
Additional Comments: I would like to have it quiet (the case is already pretty silent). The old machine in it is a Pentium E5300 and an HD4770 512mb video card. I don't mind getting last generation intel stuff (lga1156). MICRO-ATX ONLY! Thanks.
Sounds like you don't need a very powerful graphics card, it would make more sense to get a good CPU and plenty of RAM. Hows this?
Intel Core i5 2500k
G.SKILL Ripjaws X Series 8GB (2 x 4GB)
MSI R6850 Cyclone PE Radeon HD 6850 1GB
CORSAIR Builder Series CX500 V2 500W
This totals just less than $590 before $35 of rebates and shipping.
If you wanted to save some more cash though I think you could easily cope with a HD 6770 and a Corsair CX-430 PSU because games are quite far down on your list and the ones you mentioned aren't exactly taxing on the graphics card.
Civilization V is an outlier that STRONGLY favors nVidia cards, so much so that a GTX460 beats a HD6950 in that title. Doesn't CS5.5 take advantage of CUDA? That would be two strong points in favor of a nVidia card.
If you want to save some cash lower the GPU to a GTS 450 or HD 6770 imo, don't get an i3. Yes the i3-2100 is good value but you will definitely notice the difference between that and an i5 with your usage. Much more than the difference between HD 6850 and GTS 450 anyway. I'm pretty sure the GTS 450 and HD 6770 only need 1 x PCI-e connector too so you could go with a slightly cheaper CX-430 PSU.
EDIT: Just added it up, you can shave another ~$80 off by going GTS 450 and CX-430. Totals $512.95 on Newegg.
Okay, do I am pretty sure I'll get the i5 760 @ 2.8ghz and the gtx460 1gb. Im still not sure what ram I want or what motherboard.
Also, this machine will only have to last me till next year. I just needed to put a little money into a better machine because my current set up is starting to lag. I am getting into some web development, so hopefully Ill have more money by next year to get an Ivy Bridge/Windows 8 machine!