But really, it was just personal preference. Way back when I was learning 3D graphics, I found it easiest to visualize Z as elevation above the XY plane. I'd also used some software that followed that convention (like trueSpace and later 3D Studio Max).
These days, I mainly work with software that tends to favor a Y-up convention by default.
According to legend, this is why the Math and Physics departments hate each other.
X is almost always to the right, so this gives me Y and Z to work with. To satisfy both the positive values into the screen and right handedness I need either Z forward and Y down or Y forward and Z up. Since most of the time you draw a graph with an axis going up rather than down, that settles it.
It's entirely arbitrary in the end, a single matrix will fix any dispute you have amongst peers.