For a prototype PCB fab, http://www.oshpark.com is my favorite.
Edit: Also, supporting any of his efforts makes you feel good, considering all he has contributed to the EE hobbyist community (contextualelectronics.com, kicad.info, the Amp Hour podcast, etc.). He and Dave Jones (EEVBlog) are the superstars of the hobbyist community.
The thing that gets sent to the board fab is a set of files in "Gerber" format. So, the Gerbers are your last chance to confirm that the boards will be what you want. I suggest using a Gerber viewing program and look carefully at all of the files to make sure that they agree with your conception of what you expect the board to look like.
Finally, whatever fab house you choose, read all of their instructions and design rules, both to confirm that your board has a chance of being made, and because it's educational.
I've been happy with www.pcbfabrication.com for several runs of boards. I know people who go to a different house for every order, shopping around for the best price, but that just adds one more level of effort and worry for me. So I'm loyal to a good supplier.