As described in http://www.raspberrypi.org/archives/1929, there are various changes. Does this affect software that isn't using I2C or the new GPIO signals? I'm assuming I wouldn't be using the emulator or JTAG.
Nothing at that URL indicates that there should be any software changes if you are not using the GPIOs - however there is sure to be something they overlooked. We'll just have to wait until someone finds it :)
They've swapped the I²C connectors.
For I²C, this just means you need to check the revision in
/proc/cpuinfo and use
/dev/i2c-1 as required.
Or you can use
i2cdetect to look at both busses for any devices you are trying to talk to.
If you are using the I²C pins as GPIO, it's a bit worse because if you are using a GPIO library you'll have to make sure it's recent enough to check
/proc/cpuinfo and remap those pins.
The good news for some is that the 4 pins that were to be used to indicate board versions can now be soldered to and used as GPIO if you need some extra :)