Low-cost PCB prototyping
For the software side take a look at KiCAD, it's Free and runs on Linux, OSX and even Windows, it's about as clunky as any other EDA package, but you can't beat the cost and it has no artificial limitations.

For the fabrication side take a look at ITead, they do really cheap double sideded PCBs in about two to three weeks including shipping:
https://github.com/dren-dk/HAL900/wiki/Quirks-of-PCB-manufacturing-at-ITead