They count if made during regulation or in extra time. Deciding a game on penalties does not count in the keepers goals against average nor does it count as a goal for the person "scoring".
A save average is based on shots that are saved that would have gone in the net if not for the keeper. So if there were 10 shots and 2 go in, the keeper has a save percentage of 80%. To calculate a keepers gaa...... Lets say he has played in 10 games and in those 10 games 5 goals were scored. That totals a GAA of half, ( 1/2 ) a goal per game.
Hope this helps.