Clan wars do not get you Rep points; it transfers them from the fellow you kill. So the other side has to gain them from one of the other methods first in order for you to get any from killing them.
The Academy will give you 170 points from completing it, with a max. cap of 400 (10 points per level).
You gain 500 points from defending a castle, 1k (?) for taking a castle, and you lose points (not sure how many) if you lose the castle.
With the raid bosses, there's a quest the clan leader has to have (and he has to be present?). Off hand, I know of only two 7x bosses that give points.