Energy points measure effort on Khan Academy. Learners earn more energy points for pushing the edge of their knowledge. They are not a measure of mastery or ability.
As of 9/1/2013, you get points for learning tasks:
-- 750 points for each video completed
For practice problems:
Badges are awarded for behaviors - some related to points, but not necessarily (e.g., proficiencies on exercises, speed, or other behaviors like building community or engaging with computer science).