I realize that lots of people have threads and blogs about buying computers, but I've noticed that some of them are rather flawed. The most recent one I read tells the reader not to spend all his/her money buying the best computer parts out there since it's a waste of money. This is the farthest thing from the truth. If you have the money, buy all means buy the best that's out there: it'll last you a loooong time.
The key here is to buy the best that is within your budget, but with some exceptions. Before shopping for the best CPU and graphics card, you want to spend your money on the core parts of your computer that won't change very often or very much. This would be your PSU (spend as much money as humanly possible on this), the hard drive(s), optical drive (e.g. DVD-RW drive), and the case.
First I'll start with the PSU. The top brands are PC Power & Cooling, SeaSonic, and Corsair. Estimate the system you want, then use a PSU calculator to determine the wattage you'll need. Try this one http://www.extreme.outervision.com/psucalculator.jsp. It works great and is very precise. The PSU is essentially the heart of your computer: it powers everything and if it blows out because it's inferior, it could take the rest of your system with you. Also, these don't change very often, except for increasing in wattage. So if you get one that's, say, 100W over what you need, you'll be set for a long time. DO NOT SKIMP ON THIS!
Next are your hard drive(s). Using my human body comparison, this is long-term memory of the brain (don't confuse this with computer memory; they're entirely different). Many people have one hard drive because that's all they'll need. You can deal with that, but I'd suggest getting at least 250gb. Those drives are very cheap now. People will tell you all sorts of things about different brands, but my suggested ones are Maxtor, Samsung, Segate, Western Digital, and Hitatchi. I currently have a Maxtor IDE drive and a WD SATA drive. I have two because I do a lot with digital photography. If you're asking if you should buy a Raptor or SCSI ("scuzzy") drive, ask yourself this: am I an uber hardcore gamer, spending six to ten hours gaming a day? If you answer "no" to any part of that sentence, then don't buy a Raptor or SCSI. They have read time differences of about four seconds, which isn't really a big improvement. Plus, you could get a drive twice the size, or bigger, of a Raptor for the same price. There are two reasons you'll have to replace a hard drive: 1. it dies (which is rare), 2. it gets corrupted (which is rare unless you're dumb and carelessly download things).
Next is the optical drive. Right now, optical drives are changing formats to new technology, but with these things that doesn't happen often. I would suggest getting the fastest all-in-one* drive you can get. *By "all-in-one" I mean, DVD-RW/CD-RW, etc, etc (meaning +/- R, W, RW, and so forth). That's really all you'll need. And when HD-DVD and/or Blu-Ray drop in price and are more wide-spread, then you can buy one of those drives. But chances are, you'll have your old fashioned drive for quite a while.
Last is the case. There are a few things you want to look at here. First are size and weight. Your best bet is an all aluminum case because it perfectly combines light weight and good strength; for size, get either a mid-tower or full tower, depending on your wants (I'll get to that in a moment). You could also go with an acryllic case, but those are more for people who want to turn their computer into a light show that rivals Disney's Epcot Laser Light Show. The size of the case is really a personal thing. I've had a midtower for a long time and got sick of it because everything was cramped tighter than the Hulk in a leotard. So I moved up to a full tower. But if that's not even enough space for you, you could get a server tower (not sure you'd need this unless you're running a server or need numerous hard drives). The next consideration when buying a case, which is also the most important, is cooling. Check out my other blog post on the "Ultimate Cooling Case" for more info (I'd link to it, but I don't know how). This is key because you want your computer as cool as possible, especially if it's hot year round where you live or the summers get swealtering. Now, if you plan on liquid cooling, the case's cooling features are less important, if not at all.
Once you've budgeted for these things, then shop for the CPU and graphics card (RAM and mobo are least important, though they have to be compatible). These two technologies are changing faster than Stephen King writes novels. It's as though the Flash is creating all of these products. If you don't plan on upgrading or want to upgrade for a while, buy the best you can with your money. I would recommend Intel only because AMD has been flailing horribly since Intel's Core 2 came out. The question here may be, "Should I go Duo or Quad?" I recently asked myself the same thing. I decided on quad for two reasons: 1. it's super fast, 2. I won't have to upgrade for a while. This computer could potentially serve me well in most games for three years; I may just need to upgrade my graphics card. But if you don't have the money for a quad or don't see the need for one, then a higher-end Duo will do just fine.
As for graphics card, I would definitely recommend nVidia. ATI/Radeon failed horribly with the R600; it didn't live up to the hype at all, and from what I've heard/read, it's not that good. Any of the nVidia cards from 8600 and up are a good buy. Now, allow me to add a little caviat here. Up until this past May, I had an eVGA 7600GT in my rig. I was horribly disappointed with it. It came factory overclocked and didn't work right from day one. I couldn't return it, however, because I bought from a computer show and didn't save my receipt (bad idea). So that turned me off from nVidia. As a result, I bought a Sapphire x1950xt, which runs amazingly. However, whenever I upgrade my card, I'm definitely going to go nVidia unless ATI can redeem itself for the 2900-series, which I doubt.
So there you go. It's a little long, but it will take you a long way.