I recently built my own to get exactly what I wanted. I wanted a cross frame setup for light touring and commuting. One of the LBS had a Bianchi Axis, which was pretty close to what I wanted for about $1200. Except, it came with cross tires, I really just wanted 28mm tires. It came with a Tiagra 9-speed group, but I really wanted a 10-speed campy group instead. It came with mountain gearing, but I really only need a triple and a 13-29 at most. I just use a 13-26 mostly.
I shopped around and got a deal on a Surly Crosscheck. Preferred because steel instead of aluminum. I got a Campy Veloce groupset from probikekit. I got Armadillo tires at the LBS on sale. Random canti brakes online. A green Brooks saddle that matches the frame, instead of the random saddle on the Bianchi.. Open Pro/Record wheels on Ebay, instead of the cheap Alex wheels on the Bianchi. The right bars and fork for $70. Probably $60 of random stuff at the LBS. $20 to get them to cut the fork and install a headset. The Bianchi had a pretty trick looking carbon fork with canti brake mounts, lots of room, and fender/rack eyelets. I might have to get one of those eventually. About a month of shopping yielded a bike that cost $1250. I spent more, but don't have to upgrade any parts. If you have more time and are more flexible, you can probably do better.
I will warn you that you might spend money on tools. I didn't include that in the cost. I had the headset and fork installed at the bike shop because those tools are expensive. A bottom bracket wrench, pedal wrench, hub lockring driver, chain whip, cable housing cutter, and chain breaker really add up. If you build your own, you're going to wrench your own. Might as well have the tools.