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.
Stages 3 and 6 are consistently bonus levels; these have no adversary, and will either feature enemies that release numerous power-up collectibles worth 2,000 points each, or a substantial number of non-firing ground enemies that release wealth.