Outlander_04 :
Every time I have compared pre-built systems they were cheaper . The people that build them pay wholesale for parts and online retailers like newegg dont match those prices . The prebuilts also include warranties that a home made PC wont .
Where building yourself is useful is when you are building for a specific purpose like high end gaming , or a work station .
Its going to depend what the OP is using his/her computer for
Like i said, you have to compare exact specifications which means brands, models, etc and software settings. Sure they pay less money for wholesale parts but their margin is not that big, hence the price difference is not either (as long as you know where to look for those parts).
Also you have to compare the settings the system is running at, eg. a prebuilt system may include a E8400 CPU running at stock 3GHz for $800. If you ask them for the exact same system to operate at 4GHz they charge a $1,200. And that is where the big difference is. One can overclock the system himself and save $400. Sure you can overclock your pre-built (not always!! see Dell), but if it does not boot up due to incorrect settings you are screwed. You have to take the PC back and the builder will open it up and fix it for you, etc etc
Finally the only different warranty pre-built systems have is regarding the software. If Windows is not booting or anything you can take it back and they will fix it for you. The hardware always bares the manufacturer's warranty which is exactly the same whether you buy it separately or in a system. In the case of prebuilt, they do the RMAing for you, but you can do it yourself no problems at all.
One last point i remembered: Buying a prebuilt system, often they do not include the OS on a disk. That is not their fault, it is a kind of "cheating" because they do not explain to the customers that they need to buy Windows if they want to have the disk too. So the user ends up one day looking for the Windows disk because the PC is asking to copy a file or something and can't find it. You should see the frustration there...