What is the most cost effective way to produce a custom circuit board?
For cost effective, full feature software, nothing beats open source software. I use the gEDA suite of tools for my electronics designs (schematics and PCB layout) but there is also the KiCad suite which might be a bit easier to use. There are several others as well. Try playing with them and doing some layout tutorials to get to know the software.

For PCBs, you could try places like Fusion PCB or DorkbotPDX. I have also heard the previously mentioned Batch PCB is good too.

For wireless, you could use something like this bluetooth to serial converter from DealExtreme. With bluetooth, you can pair devices and then it doesn't really matter how many birds you have flying around. You could also develop a smartphone app to control your helecopters.