Money is a big part of it, too. It depends on where you live. My local shop carries mostly Specialized and SE (for fixed). That's not much of a selection and I got a better deal through BD. You can still maintain a good relationship with the LBS, just make sure you buy stuff every once in a while. I took mine in for truing and a check-up. I'll probably buy most of my parts there if they can order it and the markup isn't too high.

You could also go with CL, but again, that depends on where you live. If you live in a medium-sized town like I do, you have to get lucky.