Here are the main differences between the R3 and previous versions:
The USB controller chip has been upgraded from an ATmega8u (8k of flash memory) to an ATmega16u (16k of flash memory.) This new chip should make it easier to emulate input devices like joysticks, mice, MIDI interfaces, and keyboards (this has not yet been tested and there is no code yet.)
Analog pins 4 and 5 have been broken out next to the AREF pin to allow for I2C communication. This makes it easier for future shields to be compatible with both UNO’s and MEGA’s. Also, the power pin has been duplicated next to the RESET pin to let shields know what voltage they are running (in the case of the UNO it’s 5 volts.)
The reset button has moved next to the USB input for easier accessibility while a shield is in place.

Arduino Uno Rev3 Back with 4 new pins circled in red.

Arduino Uno Rev 3 Schematic with 4 new pins highlighted in red.

This picture shows the dimensions of the pin locations of the 4 new pins on the Arduino Uno R3
