Stages 3 and 6 are always bonus stages; these have no boss, and will either contain enemies which release many power-ups which can be collected for 2,000 points each, or a large number of non-firing ground enemies which release currency.
In the game, stages 3 and 6 are always special levels; they lack a boss and may contain enemies that drop many power-ups worth 2,000 points each, or a large quantity of non-combat ground enemies that yield currency.