I accidentally gave my 5 volt pin 9.6 volts 
My Arduino still starts, but everything near the power jack and USB jack heats up now.
The LEDs still light up as usual, but I am pretty sure something is wrong.
What is it, and how do I fix it?
And please don't just tell me that I need another Arduino
Thanks!
If you have another Arduino board you can try to move the processor from the fried board to the good one. If it works your processor is OK.
If you have a multimeter you can test if the voltage regulator is broken. if you put 7volts on the powerin, the 5V pin should read 5V, if it is higher/lower the regulator is broken
idem for the 3.3V regulator. If that regulator is broken the system might be usable with a 5V powersupply.
Does it also heat up when USB powers the system? ==> possibly the 3.3V regulator.
sofar,
Rob
I don't think that it is the voltage regulator.
What heats up first is the IC adjacent to the USB jack, and the T16 crystal.
The atmel mega8u2 is what heats up first.