Bonus points:

Locate the rooms in the ships that contain green faces on the floor.
Collect 500 points for killing them, then wait until they re-appear.
Kill them again for another 500 points.

Temporary invincibility:

Wait until 272, 267, 232, 222, 171, 161, 131, or 121 is displayed on
the counter, then collect the boxes with the question marks from the
ships.