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I wanted the pull out motherboard so I could see what I was doing!
I have had one prebuilt system (from IBM) and I can't even begin to tell you the problems with it once I started trying to upgrade it. Several of my friends had similar experiences with various different manufacturers (i.e. Compaq, Dell, HP). And looking at info online, it is a perpetual and consistent problem. If someone is never (and I mean never) going to upgrade anything in their system then they might want to consider a prebuilt system, otherwise building your own is the only way to go to avoid compatibility problems.
Another thing to consider is the quality of the components (and the companies behind them) that are going into your system. CD/DVD drives are a great example. You can get some great prices on fast no-name drives now, but if you go with these cheapies you will increase the chances of having problems with software compatability. The newer copyright features on disks don't play well with many of the cheap drives causing the software to simply not function until a fix for the drive or software comes out. Notice in the prebuilt systems there is no indication of the manufacturers of some components (a good indication they aren't the highest quality). It is often the lesser-thought-of components that the "top of the line" prebuilt systems go cheap on to save costs.
Despite what the article suggests, I can still quite clearly design a system that is equal in performance to prebuilt ones for less money, or design a system that exceeds their performance for the same price.