I always build my own computers. I personally don't trust any store bought computers because you don't know what your gettign and there is very little room for upgrades. Where as if you build your own computer the sky is the limit for upgrades. I personally stick with Crucial for memory, because they are owned my Micron who makes the memory, Asus for motherboards, AMD for CPU, and Hitachi for HDDs. Now as for video cards it depends on what you want you can go either ATI or nVidia, same with Chipsets on the motherboard.
But all of this is my personal Opinion, everyone has a different one.
*EDIT*
I always but my stuff from Newegg.com some people prefer tigerdirect.com,but I like Newegg!