If you are interested in overclocking, you may want a better HSF for your CPU. A mobo from someone other than Intel will probably have more overclocking options. Both of those could readily consume the $80 from getting just 4GB of RAM. You won't get 6GB btw; that will be a 3x2GB triple channel set which is for LGA1366 boards. You want a dual channel set, which will be 2x2GB.
Yes, you could add another 2x2GB later.
The i5 (and i3 and i7) CPUs all overclock pretty well.
If you were going to spend $200-$230 on a GPU, I'd probably suggest a nVidia GTX460, although the two games you mentioned are not extremely demanding. I tend to prefer ATi cards, particularly in your price range. If the money's there, get the HD5770. A HD5750 would be the next step down, but would probably also work quite well for you, given your 1680x1050 resolution.
Would any of your non-gaming applications take advantage of PhysX? That's another reason to consider a nVidia card (perhaps a GTS250), otherwise I would stick to ATi.
You will not need a video card cooler with a HD5770; it is efficient and stays cool.
Any of the 120mm "core contact" (the heat pipes directly touch the top of the CPU) models will be decent. The 92mm ones will keep your CPU cool enough for light to moderate overclocks, but may get noisy doing it.
I use mostly Asus, ASRock, and Gigabyte. I've also used Biostar, but not lately. My mini-ITX system is ECS, but most people are likely to suggest avoiding ECS. Some people like MSI, others hate them; I know years ago they had major quality issues, but I suspect that's past history.