This is more of a list of notes on custom PCB design rather than a proper post…
There is a pretty good tutorial on how to use Eagle on SparkFun.com. Eagle (the freeware version) can be downloaded for free here.
There is also a very useful library with most of the components available on Sparkfun.com here.
if you want to create a custom Arduino shield, a good starting point is this Proto Shield on ladyada.net.
There is a good list of companies that can produce pcbs on the cadsoft website.
SparkFun (through BatchPCB.com) and nuElectronics offer custom pcb manufacturing services; BatchPCB is basically sending everything to China and I’m assuming nuElectronics does the same.