I'm pretty sure that this question has never been answered directly, though we've had hints. What made it a "time" war, as opposed to just a "war"? Was it because any war in which the Time Lords participate is automatically a Time War? Was it because different parts were fought in different time periods, out of sequence with each other or something? Was it because special "temporal" weapons were used (eg "The Moment" which the Doctor apparently possessed?) Was it because each battle had to happen on "time" or else someone would get into trouble? Any other outrageous theories?