After learning and experimenting with microcontrollers, the concept of pull-up- and pull-down resistors has been understood and saved to my hard drive. I now understand when and how to use them, and how they work. I've mainly used pull-ups because I was taught to, but it has always seemed a little backwards to me, as closing the switch sets the MCU input to LOW. I think it would make more sense to use a pull-down resistor, so that the input is LOW when the switch is open, but that is just my way of thinking.
Your eyes have probably been hurt by my stupid statements, but in the name of a total newbie to circuit design I ask: Should I pull my single-throw inputs up or down? When is pulling down preferred over pulling up and vice versa?