"GPIO voltage levels are 3.3 V and are not 5 V tolerant. There is no over-voltage protection on the board - the intention is that people interested in serious interfacing will use an external board with buffers, level conversion and analog I/O rather than soldering directly onto the main board."
I should probably add a little guide explaining what you can do (and more importantly what you shouldn't do). Thanks for bringing this up.
While I'm plugging... It has a big brother in the works over at http://quick2wire.com/ which is pimped out with a regulator, level shifters and protection diodes. This means to address the issues you raise to make it easier to tinker and reduce the chance of damage.