It seems only proper that a secret base contains secret rooms. Here's how to find them:
Level 2: Shoot out all of the upper windows of the far back wall in the Hangar. Another can be found by shooting all the yellow barrels when you are the forklift.
Level 4: Shoot every yellow box while you're riding on the STAAR jeep
Level 5: Shoot the doorplate of the second door marked General Weatherby as the door is opening.
Level 7: Shoot all the yellow barrels at the first area where the four purple zombies are throwing barrels on the hill.