Freeman insults some soldiers by calling them "a bunch of Lemmings with machine guns."
He does the same thing with some of the scientists in an earlier episode: "Ugh, Darwin was right. I didn't realize I was working with a bunch of Lemmings."
In one episode, Gordon theorizes that he was supposed to die in the test chamber and everything that's happened since is the universe trying to kill him to put things right.
"Maybe if something teleported inside of me I'd end up like THE FLY. Help meeeeee."
In Episode 67, Freeman wants the aliens to come out and play, in the same style that Luther calls to The Warriors, sans bottle clinking.
Two towards Doctor Who near the end of the series: when dizzy on Xen, he glances at a glowing blue box and confuses it for the TARDIS for a second and calls the G-Man a Time Lord.
Gordan's Hurricane of Puns at the dam references a similar series of puns spoken by the Hoover Dam tour guide in Vegas Vacation.
Half-Life 2
Gordon describes the Breencasts as "Max Headroom for old people."
Gordon mistakes a Strider for a Tripod and is worried that he's going to be capped.
Gordon refers to the City Scanners as Servo-skulls.
When Alyx makes light of Barney's reaction to Lamarr, Gordon berates her for it, describing what headcrabs do to people as 'Mind Rape', referencing both the trope name and the series that named it.
After seeing the secret doors that lead into Kleiner's lab, Gordon starts humming the Get Smart theme tune.
Upon encountering one of the game's several platforming sections: "Playing Frogger will save your life! Especially if you're a Cop Killer."
When Kleiner tells Eli that Gordon will be sent to Black Mesa East using the same teleporter as Eli's daughter, Gordon adds a gruff "We've come for your daughter, Chuck."
He refers to the Civil Protection officers as Charles Bronson wannabes, referencing the plethora of movies where the latter played a Cowboy Cop.
When Gordon first hears about the manhacks, he imagines them as Robby the Robot models from Forbidden Planet with machetes.
In episode 4, he starts singing "Won't You Be My Neighbor?" of all things. Then the Metrocops bust in and start shooting everyone.
Freeman: Nope, you're not a very good neighbor. Too much baggage.
"This [alien invasion] is going to change science fiction forever. There's not going to be any more E.T. the Extra-Terrestrial or My Favorite Martian. People won't understand. E.T. won't be phoning home. He'll be waiting for you in a dark tunnel, ready to strangle you while he literally eats you alive. If you're lucky, he'll snap your neck first. People of the future will understand that."
"What kind of country gives its police guided missiles? That's literally more firepower than RoboCop!".
Once Gordon starts musing about gnomes (again) while prowling the sewers, he briefly hums the Underpants Gnomes' song.
Episode 8 starts with Gordon singing the Mister Ed theme.
In the same episode he speculates whether or not this future is like Terminator, but decides it's not, because "I'm seeing zero AI progress." He later tells a refugee "come with me if you want to live."
This season sees Gordon really double down on the Aliens references: consistently referring to the headcrabs as facehuggers, comparing the barnacles to xenomorphs when he sees their nested mouths, comparing the Combine's headcrab shells to Burke's attempt to weaponize the titular monsters, and so on.
"What's happening is he [the G-Man] thinks he's Mr. Miyagi, and serving me up to the police is his interpretation of 'wax on, wax off'. Because apparently surviving Black Mesa and an alien world means I need to prove myself."
Episode 19 has Freeman reference Assault on Precinct 13 (1976) albeit while being unaware of what film he's talking about.