During the scene in the tech tent where Sam uses a computer, the game Dragon Age II (2011) can be seen being played a couple times. Specifically, it's the part of the game where character Tallis, voiced by Felicia Day shows up.
The aliases Sam and Dean use are Agents Taggart and Rosewood these are the names of the Beverly Hills Police Detectives in the movie Beverly Hills Cop (1984).
Charlie says to the boys as she attempts to leave the first time "have fun storming the castle" this is a very well known line from The Princess Bride (1987), a bit of a cult classic.
Heinlein and Bradbury, both surnames used by Charlie, are the surnames for well-known deceased science fiction authors: Robert A. Heinlein and Ray Bradbury.
The speech Dean gives before running into battle is the same speech William Wallace (Mel Gibson) gives in the movie Braveheart (1995) before running into battle against the English.