The question is not straightforward. One can almost never do this comparison, because pre-built computers will protect the details of the specific componants, the motherboard for instance. When you build your own you can find out a lot about your choices on boards like this. So in the home built world you could easily consider a $50 mother board or a $150 motherboard, and based on details available in part specs or from testimonials here on the forum you might very well choose the $150 motherboard.
A person deciding to buy the pre-built because its $100 cheaper is simply doing without the understanding of the difference.
On the other hand, anyone knows that if you buy a 1000 motherboards you get a better price than buying 1....so clearly the pre-built guys (at least the big guys) can price their parts WAY below what you end up with as a homebuilder. Especially if you have to buy the most plebian aspects of a system....like case, keyboard, mouse, these things are below the radar, and probably thown in for free with dells, but you pay actual money for them in the homebuild world.
That's not an issue for most of us because we re-use those componants commonly. My floppy drive was originally out of a 486dx33 system. My case is an ATX Midtower that dates back to the start of the ATX standard.
True, when front mounted usb and audio controls came out I was jealous, but I found a cute front addon unit that keeps my case in the game.
And the final point.......I don't build my own to save money, whether it does or doesn't. I do it because I enjoy the shopping process, and the build process. I get a great rush from imagineering a system, shopping, seeing the parts arrive, and then seeing it boot after a sweet assembly success.
Enjoy!
Bob