MacWorld confirms what a lot of Mac folks have known for a long time now:

Our custom-built OS X computer was faster than the $2499 Mac Pro in all 15 of the individual tests that make up Speedmark 8: Overall, it was 23 percent faster than the Mac Pro. A few of the tests were close; exporting an iMovie project was only 4 percent faster on the Bride of Frankenmac than on the Mac Pro. Unzipping a large file archive was 9 percent faster, and running our Photoshop action script was 10 percent faster.

They do offer some caveats regarding compatibility of parts and the lack of an “umbrella warranty”. Regarding the video card: A quick Google search before the build would have negated that issue. Regarding the warranty: The fact that I can easily, quickly, and inexpensively replace just about any part in my computer (which I’ve not yet had to do, knock on wood) is a powerful counterargument to a machine made exclusively with proprietary, pricey, and hard-to-get parts.