a lot of those "white box" machines you see use cheap components or integrated components. They can seem cheaper (cost wise) than building your own machine, and yet they sound comparable to the average person that doesn't know much about computers. It may say it's an intel 2.4 GHz, but then you find out that it's a celeron style cpu and it doesn't have cache built in, so it's actually slower than a real 2.4 cpu. It could say that it has 64 meg of video ram, but then you find out the video is on the mainboard instead of a separate card, and the 64 meg it uses is shared with your system memory... so if it says 128 meg of ram, but the video is stealing 64 meg of that, then you're left with 64 meg of ram... They may also use "old stock" like older or slower hard drives, which can make the machine slower...
White Box machines cut a lot of corners to keep costs down... Depending on what you are using the machine for, this may not matter.. but it can also be a pain if you want to upgrade or change anything in the system..
I like to build my own so I know what's in it, it may cost $100 more (or even more depending what you want in it) but I find it to be worthwhile.. My sister just bought a white box 2.4 GHz machine because it was way more power than she'll need for a few years, but it seems sluggish compared to my 2000+ (which actually runs at 1.6 GHz) athlon, and to build my machine wouldn't be much more expensive in proportion to the performance difference..