One other thing that wasn't mentioned was the amount of crap the prebuilt companies put into your system. I bought a laptop from Dell a couple of years ago. Upon turning the laptop on, a plethora of offers were on my system, from AOL to Disney. All crap. I deleted all the annoyances until I thought nothing was on my computer. A check on my computer revealed 3 GB of HD being used. Since I have my own copy of XP at home, I reloaded the OS, which of course erased everything Dell put on there. After getting everything setup nearly identical to the way it was before, a check on my computer revealed 2 GB of HD being used. So even trying to erase it, Dell had 1 Gig of crap left on my drive!
But it gets better. Recently, I bought another laptop from Dell for my sister. This time, when I turned on the laptop, it wouldn't even go into the OS unless I accepted 6 months of crappy AOL internet service. I turned it off, back on, same thing. The hell with that. I reloaded that OS too, with the aforementioned XP disk I had at home. I think it's only fair to mention that both the laptops work fine now, and me and my sister really enjoy our laptops. But the point is, when you buy prebuilt, you don't own the software, you are at the mercy of the company that sold you the machine.
Building your own machine gives you the comfort of choosing exactly what gets put on your machine without any hidden programs running or being forced to accept stupid offers just to use your own PC.