Not sure on the OS - only just beginning to dabble with Ubuntu so someone else will have to comment on that.
I went for a mid-range GPU felt it gave a better balance of noise and power - Hexus.net and Anandtech.com both give good comparisons of relative performances for dif games, power draws, heat, and noise (Anandtech is more useful for the latter, giving dB values). Remember to get a motherboard that supports SLI/Crossfire if that's the route you decide to take... not that I forgot to check or anything like that
and the CPU is certainly a good one, but weigh up if you need to spend that much on it for what you want to do. Again, articles on Hexus and Anandtech will give you a good steer on comparing CPUs. Depending on whether you're willing to wait , both Intel and AMD are launching new chips this summer/autumn which are supposed to be a whole new leap in performance. That said, I upgraded my P4 2.8GHz to just an i3-540 3.07GHz (only dual core, but some reviews suggested it was better for gaming than equivalently priced AMD quadcore chips). Got it as a stop-gap while I wait til the new chips later this year, and the difference is noticeable even with this lower end chip.