Personally, I would go to a reseller as it helps them to stay in business and sell the products we all love plus it helps apple keep them certified to sell equipment since every sales counts towards maintaining their quota.
Also, I believe that resellers can order direct from Apple as well, however I believe that many of them order through channels such as EMJ as they carry a larger stock of the product and have more of them in stock than Apple who would have to ship it to you from texas. I could be wrong as I am not a reseller.
I thought you can't order a BTO box from reseller, ie if you want to get a PowerMac G5 with a Radeon 9800 or Bluetooth, you have to go through Apple. Resellers only sell standard configs, which they can upgrade (RAM, HD, airport card, etc.), but they can't add an OEM Radeon 9800 or Bluetooth.
Our local reseller is "oob", so we must order in.
A Toronto reseller, for example, must charge shipping which can add sustantially to the cost. This has to taken into consideration.
In some instances, buying BTO from Apple is cheaper as they include ground shipping in the cost. Touchy, feely, smelly advantages are lost as are service considerations.