During my LED-googling, I also ran across the Neopixel light strips. Those are strips made of WS2812 LEDs - RGB LEDs with integrated 2811 controller. Thanks to Adafruit there also is a control library, which makes it reasonably easy to control those things with an Arduino.
Here is an idea of integrated navigation and anti-collision lights for a quad:
4 segments, 1 red, 1 green and 2 white for left, right and rear arms, showing navigation colors and doubling as an anti-collision strobe. Those WS2812 are not immensely bright but hey - nobody said you can only use 3 per arm :).
And they probably work great for a plane too, just put half a meter of strip to every wing. That IS gonna be bright.
Here is the final version which I will install in the copter. A few more programs and the whole thing is controable via the RX.
I'm also currently thinking of making a version that's controlled by MAVlink.