Hi,
I stupidly put too much current through my Arduino Micro by hooking up a 9V battery to 5V instead of Vin. When I plug it in, the blue light goes on so it still has power but the serial port is not reading it. The reset button also doesn't work. Is there another way I can rest it or is it a goner? 
It's likely a goner, not just the mega chip either. Sorry.
Did you see any Magic Smoke™ escape?
You won't always see smoke.
Applying 9V to parts with absolute max of 6V for Vcc will damage them.
The power LED is likely rated for 20mA, I think it has 1K current limit resistor. With 5V, likely sees ~ 2mA, with 9V maybe 6mA, so that part won't fry.
Talk about 'luck of the draw'. In another thread someone connected the +/- pins on his motor board back to the Arduino not realizing they were unregulated and connected to a 12V/8A supply. He reports that though it killed his USB to his computer and his monitor wouldn't work, the Arudino survived.
He knew pretty quick something was wrong and unplugged it. How long did you have your setup engaged?
outofoptions:
He knew pretty quick something was wrong and unplugged it. How long did you have your setup engaged?
Components can die in the blink of an eye.