I have a load of stories I can tell about my quadcopter project(s) as well!
I managed to kill not 1... but
2!! microcontroller boards, due to the same mistake that occurred in different ways. The microcontroller board in question is essentially a modified arduino a few sensors on it. Called the Multiwii board.
I had a ratsnest of wires of the quadcopter wired up on my bed and was working on fixing the frame after a crash. The Multiwii board was mounted directly on top of the power distribution board, which connects to a 3S LiPo battery capable of delivering over 1KW. While it was apart, some guests arrived and I left the board alone next to the distribution board while still connected. When I came back and hopped back on the bed it moved just enough to short out and many wires went up in smoke, along with the multiwii.
Then I had another incident where my OSD display was not functioning properly. Strangely it worked whenever I got my scope out and hooked up the ground. As soon as I disconnected the video out from it back to the transmitter I did not have an OSD overlay from the camera video, or that the picture was really fuzzy, I don't remember anymore. I realized an hour later that while video was being connected, the ground was not connected on the OSD board!
Well I connected it up to 12V as the board requires 12V to go into a small 5V switching regulator, but I had the plug one pin over too far, so the grunty 12V from the distribution board shorted to the ground on the board. It blew the board, as well as the main multiwii board.
After receiving the replacement boards, I rewired the whole thing so that the minumOSD board no longer required 12V.
more recently, I was rewiring the quadcopter and my hands slipped and well same as before 12V got connected to ground, causing a whole bunch of wires to go up in smoke. At this point I was so frustrated with my clumsiness and having to keep buying replacement parts. I mean, I literally just fried the minimOSD board, the multiwii flight controller, a I2C to UART converter board, and a GPS module, literally everything!!!
Once I recovered from my mental breakdown, I decided to make my own flight controller board with a old dusty arduino I had lying around. To my amazement, although I killed the ATmega328 chip on the board, a small low dropout regulator (which sacrificed itself) protected all the sensors. I have a box of shame which all dead electronics go to in case I need them later for some reason. Furthermore I discovered that the GPS module that smoked when I tested it by wiring it to a USB FTDI adaptor only smoked because a reverse polarity protection diode which blew and shorted. After desoldering and replacing it, the thing worked fine! And because my arduino mega has more available UARTs, there was no longer a need for a separate board to allow the UART GPS to interface to the multiwii! And not only that, but the mega, due to it's increase processing power, allowed me to enable more features in the later releases of the multiwii code, such as navigation!!! So it turned out to be a win-win!
So after all that, my quadcopter is now a simple DJI flamewheel frame with a arduino-mega double-sided sticky-taped to it, with a rat's nests of wires going every which way, as well as a plastic cutout mounted on top of it with holes for the standoffs for the old multiwii board, some wires connect the I2C bus on that board directly to the arduino mega which allows sensor data to be collected by the mega. Directly on top of it I have the GPS module mounted with more wires going to the mega, and I had then cut out a small perfboard and mounted four servo headers for the 4 ESC's (brushless motor controllers). It's a ridiculous mess but it WORKS!!! (well, most of the time, anyway.)