"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.
Or you could do something like this:
The cheapest way to get A/D is to add a bunch of resistors via a summing network to one input of an op-amp and the other input to the signal you want to measure. The output of the op-amp goes into one of the digital inputs. Binary search across the output bit combinations to find the point where the input bit swings. This you can do for pennies.
Lots of options to add analog without having to add an arduino.
A simple PCB in the picrust form factor could implement a high quality multichannel ADC IC, with no microcontroller programming required.
And as a bonus, you'd be able to design it with sane connectorization for your actual application. (eg, appropriate scaling resistor your sensor, tidy two-wire plug or screw terminal, etc)
I'm very pleased that the RPi has stayed focused on not being everything to everyone, and has left these specialized applications to be implemented as peripherals.
But yeah I'm also "missing" a $10 breakout box with a few in/out pins and some glue logic, and the peace of mind that I won't fry the Pi if I mess up.
One big plus seems to be cheap/easy duplication of GND and V+ pins.
OSHPark now sells the bare PCB for $4.60: http://store.oshpark.com/products/pi-crust-v4
There's a Google Group to discuss ideas, etc:
(Failing that, there are a variety of I2C/SPI to UART chips around. Here's one: https://www.sparkfun.com/products/9981 with SparkFun's usual 1495% markup :)