Nothing wrong with eMachines (I had one) or Semprons.
Nice mini case, there.
Core 2 Duo is the winner of the CPU race for now. It's the fastest, period. AMD is still a great CPU, though, as well as my favorite.
Check around in the General PC's and the High Performance PC forums to see what aothers are buying/building, as well as a few tutorials (with pix). Then, if you have questions or need recommendations, don't be afraid to post a thread.