It is preferable to use resistors on all the pins, because you can still use them in your software, and having GPIOs permanently hook on VCC or GND can destroy them if by mistake you set them as output.
An good example of multiple purposes is to use GPIO2/GPIO0 as I2C bus, because I2C bus also requires pullups and therefore it is a perfect match with those GPIOs.
GPIO15 can still be use to blink an LED for example, as long as it has the pulldown required.