A console during one of the minor boss fights reads "Gearbox" and "Valve". Valve developed the first Half Life game, while Gearbox developed the expansion packs "Blue Shift" and "Opposing Force".
Several points in this add-on pack show places or situations from the original Half-Life: During the opening titles, the Osprey plane flies by a section of mountain from Surface Tension. On your way to the extraction point, you travel through parts of the train ride areas from the opening titles of HL. Once at the extraction point, you get to watch the officer making the radio transmission to Cooper (a marine who is situated by a tactical map in Half Life) regarding extra air strike targets from the end of Surface Tension. After the "We Are Not Alone" chapter, you find yourself in the teleport room from Half Life's Lambda Core chapter, just as Gordon Freeman is going to Xen. On Xen, you can use your new found Displacer teleported gun to transport yourself to the Hazard Courses (training courses) of Half Life, now infested with aliens.
At the beginning of the chapter "We Are Not Alone", at the opposite end of the blast doors that lead to the Lambda Core's portal room that Gordon takes to enter Xen, you will see a vent above of you. If you shoot this vent with any weapon 25 times it will break, releasing a harmless creature known as a Chumtoad. These creatures were cut from the game, rendering them useless. But their intended use was for bait (hence their name) for the creatures of Xen.
In the chapter welcome to black mesa in the exit of the medical labs the player can find a computer.
If the player uses the use key on the PC it will crash and display a blue screen.
At the beginning of the chapter Pit Worm's Nest, the trash compactor room is exactly modeled and a reference to the famous trash compactor scene from Star Wars - Episode IV: A New Hope.