Our team doesn't use any circuit boards. Every signal carrying wire connects a device directly to the RC. And the rules in the past were very clear about high current wiring.
But back in college, the most popular company for that kind of thing was
http://www.pad2pad.com. They provide software that can give you quotes as you design. They are reasonably priced for low quantity pcb production runs, but the price totally depends on what you are looking for: how many layers you need, and whether or not you need solder masking. Most of the people I knew would spend around $200 or $300 for boards for senior capstone projects, but that includes extras, which lower the average cost of each individual board considerably. So price is
extremely dependent on what you have designed.
Customs PCBs can certainly save a lot of time and reduce points of failure. And they make a project look more professional.
Good luck,
~Phil