The answer depends on what you want the "default" configuration to be. For example, say you have a down-stream N-channel MOSFET, and you want it default off. Then you would use a pull-down resistor to ensure this behavior if the input becomes high impedance.
simulate this circuit – Schematic created using CircuitLab
On the other hand, suppose you have an upstream P-channel MOSFET, and want it default off. This time a pull up resistor is required to create this behavior.
simulate this circuit
There's also the alternative case where you want a device to be default-on, in which case the above two cases would be reversed (pull-up for the N-channel MOSFET, pull-down for the P-channel MOSFET).
A few other considerations:
I2C lines specify pull-up resistors because devices are "expected" to have an open-drain to ground, and thus need some way to raise the line potential.
Analog comparators are usually configured as open-drain devices, and thus also need pull up resistors to get a high potential output.
You may draw more current using pullup/pulldown resistors, depending on what's hooked to the input/output.
Either configuration could works equally well in your application (i.e. there's no significant advantage one way or the other).
... And any number of very application-specific reasons why one configuration may be preferred.