During a long career as a reviewer, I've dealt with a lot of boutique builders. In this article, I describe five of the best that I've found: , , , and .
Unless you're looking to buy a stock system off the shelf just for the logo, the main reason to go to one of these sites is to get exactly the type of high-end system you want for gaming, for video development, or just because you like the bleeding edge. In that case, it's best to configure a system at two or more of these vendors, so you can decide which builder comes closest to the configuration you want (not all will install components that they normally don't stock or sell), and which offers you the best price/performance ratio.
If you're wondering whether the builder you're thinking about is on the up-and-up and not just some fly-by-night sleaze looking to pocket your cash, the easiest way to find out is to look at the company's track record. This is where online social networking can actually come in handy. The users of these companies tend to be very active online, both complimenting and dissing the vendors they've used. If there's no buzz about a company, you might want to step back for a while -- the company may be too new to judge.
And remember: The devil is in the details. After you've configured your ideal system at two or more of these builders, also compare the warranty and support each company offers. It's unlikely that you'll be able to get a highly customized PC reliably diagnosed and repaired anywhere but where you bought it.