I have built my last 3 bikes, yes they each cost me a bit more than the pre-assembled. But taking the touring bike I am just finishing, building your own gives you quite a bit of freedom in component choice. If I were to take the the pre-assembled bike and swap out the parts I felt were essential to have the price difference would be much closer. But again building my own will cost a bit more.

I just like being able to pick the hubs, spokes, rims, headset, ect, ect, ect. Plus there is a bit of reward knowing the ride between your legs was put together with your own hands. Not to devalue the pre-assembled or LBS assemblies. The guys at the local shops will always get you the best bang for your buck.