I've really found that the only time it's cheaper by any significant margin is if you are using an open source operating system. 12-13 years ago I made a decent living building systems and selling them in small newspaper classifieds (i was 14-15), and back then the profit margin was much higher. The problem with that business model was that I used one copy of Windows 95 on all of them. If i was packaging them with the OEM version, I still would have made money, but now I don't think so. Dell and it's competition get so much cheaper pricing by buying in bulk that it just makes up for it. Another thing is a company like dell can have sick warranties. So most of the time when people are comparing these prices, they aren't comparing apples to apples.
Quick Dell Warranty Story - My younger brother packed up and drove back to college after the summer of 06. During his drive he fell asleep, the car rolled and the laptop was tossed from the car, and no one at the scene noticed. Someone eventually found it, and contacted dell with the service tag #. Dell sent that person a box with paid shipping. Dell received it, took the hard drive out, recovered the data, and put it all on a new hard drive in a brand new laptop. At this point they called my brother and told him the story and said that the laptop was being overnighted to him. That's an amazing warranty and amazing service if you ask me.