Someone answered this recently as a by-the-way on another thread: I think it was AWOL or Grumpy_Mike.
IIRC, the second method is preferred since it sinks the current to the i/o pin, but I daresay someone will confirm that (or tell me I have that back-asswards). Yes the programming is less intuitive since low is "on" but that so-called "active low" is common and easy to cater for in code anyway.
But the order of led-resistor or resistor-led matters in neither case since it's a series circuit.