There are several websites to help you pick the parts and customize a computer solution that is tailored to your needs.
To get started you'll need to decide a couple of things based on what functions you want your computer to perform. Case form factor is one. Do you need a full sized case or would a smaller form factor work well? You'll wrestle with the cost savings of AMD vs the speed and cooling if Intel processors.
Here are a few websites I've used to custom configure my new computer.
PassMark Software frovides wonderful cost vs performance charts for CPU's and video cards.
Once you've got an idea of the processor and video card (if needed) you can easily configure a pc using http://pcpartpicker.com This website does many wonderful things. You can browse other people's builds, create your own and share it with friends, and see current prices and sales. As an added bonus it checks to make sure everything you pick is compatible with the rest of your build.
Finally, you can order your parts and dive in, or pick a custom builder locally or online. Several companies like www.ibuypower.com and http://www.cyberpowerpc.com will provide customizable solutions for a variety of builds.