While wiring up my new Arduino Uno R3 on a proto-board, I accidentally shorted the 5V pin directly to Ground. The LED's immediately turned off and connection was lost. It was powered by USB connection. After 3-5 seconds I removed the short. The LED's have remained out, and I haven't been able to reestablish connection with my computer since. I've unplugged and re-plugged the USB cable and tried the re-set button plenty of times. This short shouldn't have fried the board... what happened? How can I get my Arduino working again??
Have you tried restarting the computer? The computer will shut down the USB port to protect it from a malfunction like this (over-current).
You can also try the ports on the other side of the computer (or front/back) as they're usually on different controllers.
The genuine Arduino boards feature a digital (temperature based) fuse.
When shorting an Arduino, it will heat up the fuse on the Arduino. When the fuse gets to a certain temperature, it will automatically cut off the power from the USB connection to the Arduino board.
When the fuse cools down, it will conduct again.
The motherboards of most computers these days also work with these digital fuses, so you might have heated up both. It wouldn't hurt to reboot the PC and disconnect the Arduino and give it a minute to cool down.
If it still doesn't work, you might have fried the Arduino or the specific USB port. Try a USB port that is likely not connected to the same USB controller in the PC. Meaning, don't just try the first USB port next to the one you used, but try a USB port on the other side of the PC / laptop, they are likely to be connected to different USB controllers.