In the "Black Project" mission, where you have to infiltrate Area 69 and steal the jetpack, at one point you pass an inaccessible room with a bunch of tables in it. On one of the tables is a red and white crowbar. This is obviously a reference to the game Half-Life, in which it is Gordon Freeman's signature weapon.

Plus, Area 69 is very similar to Half-Life's Black Mesa Research Facility (both of which are based on the real-world Area 51)