The problem with choosing contractors is that 90% of them are theives. When you go for the big builders you trade in half the theivery for 50% lower quality work. I can't tell you how to pick a contractor. Myself I would do the general contracting myself and handle everything (it requires a lot of time), General's typically charge 5k-15k (that's a lot of savings). Finding good contractors and sub-contractors is generally really hard to do.
The general rule of thumb I have heard is find a good honest drywall contractor and ask him about good framers. Use his recommendations to find a good framer and ask the framer who does good foundations, etc...
If you do the generaling yourself be prepared for a lot of hassle with guys that say they will charge $x, then end up charging you $y and not finishing the work. (and never ever pay them all the money till they are done, in fact never give them enough money that it's cost effective for them to cut tail and run on you).
The big thing you need to do is start asking around. Talk to people that have built recently, hang out at home depot. And DEFINATELY educate yourself about the costs, risks and what you want BEFORE you start.
PS always ask for references and call the references and ask detailed and pointed questions about their satisfaction with the work, ask if you can come by and look.