Since I'm a big geek, I love sitting around and tinkering with my machines, so I'd definatley say building it.
The advantages are you knw exactly what's going into your machine, and you know how to fix any hardware problems that may occur.
Cost-wise you can save around 1,00-1,800 on price by building it yourself and buying the parts, but that really depends on what you purchase. if you purchase high-end stuff, it might costy you around the same but only if
all you purchase is high-end stuff.
Factory made depends ony our uses. Factory made machines aren't generally good gaming machines, but are good for E-Mail and internet pruposes and usually good for uploading pictures from cameras, although if you have a higher-end camera (like those new DVD Camcorders), you'll need a Hi-Speed USB Card to upload those.
That's just my 2 cents, and I'm still learning about hardware and such, so you might be better going with someone else's advice, although I got the info from 2 of my uncles, who both know a lot about hardware and computers, so, your choice.
-Frank
EDIT - oops, too late, posted this before reading yours. Congrats on your new comp...I guess =/