I started this build a few months ago and have slowly been adding to it and changing things. I wanted something that I knew would keep me relevant for a while but at the same time still be able to meet all my needs. I started by upgrading the motherboard, RAM, processor, and heatsink. About a month later I got a new case and graphics card. At this point, I'm not really sure what the order was of getting new parts but here's my current build.
Motherboard: I went with the Gigabyte 990FXA-UD3 simply because I liked the muted black and grey accents. The board looks super clean even without anything attached to you and then you don't have to worry as much about finding matching parts based on color. So, ensuring that you don't automatically bottleneck yourself with the FSB is nice. Side-facing SATA ports helps with cable management and keeping the look of things pretty clean.
FX-6300: Price. What sold me on this processor is getting 6-cores and a solid 3.5GHz out of the box that you could easily overclock up to 4GHz. I know games aren't utilizing the extra cores quite yet, but having the available options should give me some pretty solid performance over the next couple years before I upgrade again.
Case: The Fractal Design Define R4, while a couple years old now, is an incredible case. The included silencing material does wonders for cutting down on overall noise. Their Fractal R2 fans are incredible in the amount of air they pull through the case despite running at lower RPMs. I moved the included black fan up to the front and added a white to the back to help bring a bit of color to the otherwise dark case. Also, 140mm fans are so much more efficient than their 120mm counterparts.
Corsair H100i: The amount of customization involved in this closed-loop system is pretty impressive. Corsair knows what they're doing with their components and exactly what their enthusiast buyers expect out of their products. This is my first time using a water-cooled heatsink and the install was flawless. To make sure you keep things looking clean, make sure you do some test fitting before you wrench it down. Run your cables to the USB port and the fan headers before you attach the waterblock to the CPU. This will help you maintain your clean cable management and help with some of the frustration that you WILL encounter.