I always just let the computer calculate the average. I never put too much thought into how it's math works. Funny thing is, the longer the ride, the more that calculated number seems to gravitate towards a certain number. It just seems like when I add more distance, the number of stops, number of uphills, downhills, etc. just seem to average out so that the longer I go, the closer I get to this one number (it happens to be 16.4 mph).
While I generally have started to relax more and smell the roses, there are always days when I feel like want to do nothing put push push push. On those occasions, if I'm shooting for a certain higher average, I'll take into account the potential stops and push harder in the flats to compensate for it. A poorly timed red light can easily drop .2mph off of the average. But it's included in the computation because I really was riding slower for those 100feet or so.