There are several downsides to buying a pre-built PC that far outweigh the money issue.
The use of proprietary parts (think Dell/eMachines PSUs) makes replacement/upgrading difficult if not impossible.
You don't get an "install" version of the OS. Most (if not all) manufacturers now include an image of your install (and many appropriate a partition on the HDD to store it). These images are preloaded with all sorts of useless advertising crap and "trial versions" of programs you wouldn't want anyway (think AOL).
Contrary to popular belief, most manufactered PCs carry only a 60 day warranty- anything more must be purchased. Because they are using "OEM" parts, you could be SOL if anything breaks after two months...even a part like the CPU which normally comes with a 1 or 3 year guarantee, is limited to the 60 day period. Could be expensive if something big goes...
Manufacturer software support is notoriously crappy.
Your motherboard may be physically capable of using a dual-core processor but if Dell doesn't see fit to release a BIOS flash to support it, well, too bad.
All in all, if you are capable of building your own PC (and most folks are) you should do it.
Assuming you pick the right combination of parts (which is the hard part of the whole deal anyway) the chances of getting exactly what you want (and being able to deal with it for a few years) are much higher.
But you knew I'd say that, didn't you?
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