Maybe start with Newegg and tigerdirect ?
http://www.newegg.com/
http://www.tigerdirect.com/
I've used both for parts, Tiger for a barebones back in 486 days...
ebay is ebay.
Cross check on amazon.
Also, if you can make a barebones work then also look at manufacturer refurbs. Get a MB/CPU/Disk/Case/Memory config you can live with. Swap the PSU and Video. This approach gives you a clean windows license and is usually cheaper than parts from scratch. If you have a particular MB in mind, or want to OC, or are fussy about Case then you may not want to get a refurb.