I have to totally agree with Lephturn.
However, I will put in my own $.02
I bought a Dell, was able to put in pretty much what I wanted (go to the webpage, and customize your computer, or call them. I found them to be very helpful and knowledgeable. WAY different than your average boxed computer company). It has been running pefectly for almost five years now. It doesn't even crash ever. It has run so well, I bought another a few months ago. Sure, my company paid for it, so I couldn't build it myself, and DELL is, in my opinion, the finest computer you can buy. My advice is, if you are going to buy a boxed computer, go with Dell. They put top-end components in their machines, you can pretty much put what you want in there, they will last forever. I opened my new machine up when I got it home, and it is very nice inside. Lots of expansion slots (no PCI, though who needs them anymore) lots of room for more memory (I got 256 megs) the case is excellent, everything is great. I would say, though, that you do need to re-format the hard drive so you get the junk off of it. Dell sends all of the software, so it's very easy to re-install only what you want. I can't say enough good things about dell. You do pay for them, though, and that's where you need to decide if it's possible you have enough knowledge to trust that you will make smart desicions when purchasing components. You will save loads of money, but you need to be careful to get quality components that aren't going to fizz on you in a year, or sooner. It is not worth the money you save if it just craps out all of the time.
If you do end up buying a boxed computer out of a store, I really do not think you will get a good deal, period. You will get screwed, either by paying too much, or with crappy components. The day is gone where you can go out and buy a good machine off the shelf.
Good Luck!
-Greese