I never have the time to search around/research new hardware or good deals, so lately I've been lazy and just used the
www.pcpartpicker.com forums. I just look for the price range/type of build and then the highest rating and basically buy everything from the links in the pcpartpicker profile. If it's recent it's usually pretty accurate with shipping and deals. The last few builds I've had fairly good luck with this.
Here is a random example I selected, I haven't looked at it so it might not be recent, it was just the first I saw in the forum:
http://pcpartpicker.com/p/1Ve6j
Some of the builds are garbage though, so I usually wait until I find one that everyone is rating high and positively commenting on.
While building and making sure parts are compatible is fairly simple these days, finding the good deals on the hardware seems to be the main goal of most builders now, and this site helps out since people are always scouring hardware sites and posting builds.
And of course, I'll mention the obvious argument of custom vs. prebuilt....If you miss out on deals and end up spending too much on a custom build it's kinda pointless since you could have just bought a pre-built one and saved yourself money and the hassle (and probably got a decent warranty with much simpler rma support). And it's easy to spend more on a custom build, especially after you start throwing in the cost of the monitor, kb, mouse, etc...(if you need those items)