Over the last several years I've been able to put state-of-art computers together for myself, family, and friends for about $600 - $750, excluding monitors, mainly from parts bought at MarketPro shows around the D.C. area. I'm guessing that the little Ma & Pa stores that put systems together have to buy more parts than they need to get good price breaks, and then sell off the excess mother boards, disks etc. etc. at the shows. Flat panel monitors or anything terribly unusual could be bought from pricewatch.com or ebay.
By contrast, the computers I've seen being sold at stores for under $1000 have always appeared to be things which have sat on shelves for a year and a half or more and are not fully up to date.