SexyGuy, congrats on deciding to do this, even though there are some questions or a learning curve, it's a lot of fun to spec out your components and you will learn so much in the process - including the tweaking and hitting up forums, etc. after the system is built to share any experiences or tips of other users. And they say there's nothing like using a computer that you put together yourself, it's a certain kind of satisfaction there when you built it from the ground up, installed the OS yourself, etc.
Saying that, I can see where both GiancarloC and csb999 are coming from with each of their two posts directly above because I'm sort of conflicted on those points myself.
I've built/upgraded a few of my own systems over the years, but manufactured PC prices with decent specs (even specs that most totally average users might never bump up against their limitations of), are so low because consumers demand/expect that, and it's said makers are actually not making much money in this space of the market - they compensate with crapware/trialware loaded down on a new system, or chopping of thorough support (offshoring, unless you pay extra for "premium" level, etc.). I think it used to be more expensive to buy a manufactured PC than assembling your own with same (or even better specs) but over the last few years because of their buying power as organizations and bulk quantity agreements they can make with RAM suppliers, hard drive suppliers, etc. I believe in many cases a system with comparable specs is the same or even cheaper than doing it yourself.
Maybe more importantly than price though, csb999 raises a point that has frustrated me as well. In the PC space, obviously quite unlike Mac hardware in that it's quite open, I got tired of weird little incompatibilities about this version of a motherboard's BIOS, against this processor, against this video card graphics chipset - sometimes seeming like I was the only one experiencing it (or finding a handful of other souls online that happened to be running the same combination and finding the same things), or at the mercy of the manufacturers, waiting for a BIOS/firmware (or software driver) update that was very slow (or might not come at all) while they pointed fingers at the other product as the one with the issue. When you throw Windows into the mix at what it will and won't support and how it operates on top of this hardware, that's adding another compilation. I think on one hand with SexyGuy wanting to run Linux you can keep Windows out of the equation; on the other hand, with Linux you'd have to be sure all your hardware is supported with correct drivers, etc. and the userbase isn't as wide (although growing all the time). csb999 aptly points out that with a manufactured system, thousands of other users would have the same model/configuration so the broad userbase helps in that if there's a known issue, the manufacturer would be more likely to get on it and offer an update - mind you, unless they consider the model obsolete/out of production and don't want to support it. There are pluses and minuses either way to building your own vs. buying a complete system!