In what situation would the Vin pin be attached to any of the I/O pins?
Vin is exactly the same as using the barrel jack (DC in) on the Arduino.  You can use it when you want to power your Arduino from an external source and you don't want to have the bulk of a big power plug.  It can also be used as a power output when you are using the barrel jack, for instance for powering relays or motors.  It just saves on having to splice wires into the cable of a wall wart, for example.

The voltage you feed in to the Vin pin should be of the same specification as the barrel jack - that is, between 7 and 12V.  From there, just like the barrel jack, it goes to the 5V regulator to provide the 5V for the board, and then on to the 3.3V regulator for low powered peripherals.

If, at any time, you power the board from the USB and have something connected to the Vin pin that consumes power you risk damaging the 5V regulator on the Arduino since power will flow backwards through it form 5V to Vin, which it really isn't meant to do.  In these situations it is good to connect a diode between 5V and Vin such that the anode is on 5V and the cathode on Vin - so that if the 5V is higher than the Vin voltage then the current will bypass the regulator safely.