The new Mega 2560 R3 includes all the features of the previous R2 board, but now uses an ATMega16U2 instead of the ATMega8U2 chip. This allows for faster transfer rates and an increase in memory. No drivers are needed for Linux or Mac (inf file for Windows is needed and included in the Arduino IDE). It also gives you the ability to have the Mega show up as a keyboard, mouse, joystick, etc.
We use these Arduino compatible boards here in the shop on a daily basis so we can attest to their high quality and usability first hand.
The Mega 2560 R3 adds SDA and SCL pins next to the AREF. In addition, there are two new pins placed near the RESET pin. One is the IOREF that allows the shields to adapt to the voltage provided from the board. The other is a non connected pin and is reserved for future purposes. The Mega 2560 R3 works with all existing shields but can adapt to new shields which use these additional pins.
Revision 3 of the board has the following new features:
Operating Voltage: 5V
Input Voltage (recommended): 7-12V
Input Voltage (limits): 6-20V
Digital I/O Pins: 54 (of which 15 provide PWM output)
Analog Input Pins: 16
DC Current per I/O Pin: 40 mA
DC Current for 3.3V Pin: 50 mA
Flash Memory: 256 KB of which 8 KB used by bootloader
SRAM: 8 KB
EEPROM: 4 KB
Clock Speed: 16 MHz