From my understanding, you can almost always get a quieter machine by building it yourself. That's because you're allowed to do crazy things like install ducts, suspend hard drives, etc, which can be ugly to look at or dangerous to ship.
That said, sometimes it's a lot easier to get someone else to assemble it for you. I would recommend looking into Arm Systems
, the makers of the Stealth PC. They've earned an SPCR seal of approval for quiet PCs. But they're not quite as quiet as the homebrewed PCs of the SPCR staff members (but they're very close). So really it comes down to how far do you want to go vs. how good are your skills and how much effort are you willing to put into it?