New frame, new wheels, new parts, all-new bike? Your gonna pay a lot more if you build from scratch. The bike companies get ridiculously low pricing on parts... they're buying tens of thousands of, say, rear derailleurs at a time.
That said, if you know what you want, and the big guys don't make it, the gap can close pretty quickly. If you take an off-the-rack bike, and change bars, stem, saddle, and gearing, you're likely to get close to breaking even.
If you buy used parts, closeouts, hit the co-op, trade your local shop rats beer for take-offs, etc, you can make a rad bike for not much bread. There's a bunch of reasons that the folks at your shop all ride frankenbikes. (Many of those reasons can be summed up in one word: "poverty"... but also bike shop people tend to be bike nerds.)
Being OK with one less cog in back can save you some serious coin.
Lastly, a built-up bike is always cooler than a stock big-brand bike... especially to the person riding it.
--Shannon