The ending song jokingly and mockingly references Black Mesa. Songwriter Jonathan Coulton also namedrops another of his popular songs, "I Feel Fantastic".
Black Mesa is also referenced in several slide shows left running in staff areas that are accessible or at least you can see into easily.
Doug Rattmann's den in the Companion Cube level also contains a rather well-hidden shout out to Isaac Asimov's short story "Escape". His dens all have some poems altered to include cubes and the like. Here is a full list of the graffiti drawings.
"Delicious and moist" cake was originally a line in Psychonauts, also written by Erik Wolpaw.
In the testing room for military androids, GLaDOS's dialogue implies that robots and androids are programmed with a belief in "Android Hell" in order to ensure their compliance. This shouts out to Red Dwarf, wherein robots and androids are programmed with a similar belief in "Silicon Heaven" for a similar purpose.
You can find a drydock, with a life preserver titled "Borealis" next to it. The Borealis is where Gordon Freeman will likely go next in the series.
Cave Johnson implies that Black Mesa has stolen more than one of his inventions.
Cave Johnson: Black Mesa can eat my bankrupt- Caroline: Sir? The testing?
One of the displays in the old Aperture Science lobby also holds a series of awards. One diploma for the #2 spot on the top 100 list of the applied science companies of 1949, and two trophies (from 1952 and 1954) for the runner up of the "US Dept. of Defense Contractor of the Year". No points for guessing who took first place.
Another Asimov reference states that all lethal military androids have been taught to read, and given one copy of the Laws of Robotics. To share.
There's a science experiment that resembles a Flux Capacitor.
The trailers show a line-up of turrets, one of which proclaims "I'm different..."
GLaDOS says "Yesterday I saw a deer" at one point, referring to The Dandelion Girl.
In the ending, something flat (the monitor screen) flies by and Wheatley drifts forward, much like The Twilight Zone (1959) opening credits.
Caroline's line "Goodbye, Caroline!", to Laugh In, which always ended with "Say good night, Dick!" "Good night, Dick!". Ironically, it was likely intended as a Shout-Out to the The Burns and Allen Show instead, since legend has them ending the show with "Say good night, Gracie!" "Good night, Gracie!". However, Burns and Allen never actually used that line. Burns and Allen would have been on the air when Cave and Caroline made their recording, and Laugh In did not start until 1968, so it's more probable that the writers meant it to be a Burns And Allen reference.
In one of GLaDOS's new test chambers, she says that the test chamber Chell is in requires explanation. Being GLaDOS, she gives it rather quickly, and then tells Chell to "remember what [she] just said in slow motion." If you actually do slow it down, you'll find out that is actually a passage from Moby-Dick.
Screaming, "I AM NOT A MORON!", reading philosophical books, and basically being a vengeful idiot who thinks he's a genius, yes, Wheatley has more than a little Otto in him. Confirmed by Word of God.
From the Blue Screen of Imminent Death: "OPERATOR ERROR. MOLTEN CORE WARNING."
Rick, the Adventure Sphere says that he's got a belt in just about everything, from Karate to Larate.
One of P-body's dances makes her do a spinning dance, before stopping and shooting a Portal straight forwards. This may be a reference to the dance the Wizzrobe from The Legend of Zelda: Majora's Mask performs before attacking Link.
Cave Johnson's name might have come from that of one of the characters in the 1981 film The Bushido Blade.
If you let Wheatley talk long enough in the Neurotoxin Control Center, he'll try to distract the computer by mentioning a bird with gorgeous plumage.
The achievement for smashing all of the monitors of Wheatley is "Smash TV".
In the two player game there is a sequence where one of the players has to go across a path while the other player throws switches to raise and lower platforms for them to get across. This is how the old NES game Gyromite was played, wherein your robot friend would appraise the situation and raise and lower platforms for you to walk across.
At the space scene after the credits, the first thing we see is a TV screen floating around that looks suspiciously similar to the Monolith.
Portal 2 Perpetual Testing Initiative
In the YouTube promo, Cave Johnson starts off talking about his father, "a Professor of Farming at the local Farm College." Cave Johnson's voice actor, J. K. Simmons, appears in a series of commercials for Farmers Insurance as a professor at the fictitious "University of Farmers".
And in another they successfully create psychics who blow people's heads up. Cave gets back at them by taping their paychecks to the negotiator's head in a psychotic act of Crazy-Prepared.
An...altered version of Wuthering Heights gets a mention (specifically Heathcliff fending off the titular moonbase from vengeful poltergeists. Virginia Woolf and the Brothers Karamazov get a name-drop too, as part of computer!Cave's boredom-staving exercise of adding Ghostbusting to every work of fiction.
And there there's "Cave Johnson here. Just a reminder that the core goal of Aperture Gas-Finding Science is to find gas, so make sure you let us know if you see any. If we meet our quarterly gas-finding target, I promise you we will don our bondage gear, fuel our death cars, and drive around in circles, whooping it up and shooting arrows at people. Who is ready to rule the wasteland? Alright, start looking". Mad Max anyone?
And then of course, there is Smokey and the Bandit Cave, who has you test on your own while he goes to Texarcana and back in 28 hours.
One universe finds itself stuck in Invasion of the Body Snatchers, though Cave decides to do nothing about it, because aside from the kidnapping, they're pretty much harmless. If the worst they can do is gestate glassy-eyed Yes Men, then bring it on, Bug-Eyes.
Another universe features a demented Cave that sounds like he's staring at you from under a sewer grate, threatening to dismember you.
One of the universes has Cave running testing on a satellite orbiting the Earth and trying to discourage test subjects from trying to discover the "big conspiracy" (which is that they are in space) because they keep breaking through the walls, probably a parody of Dark City.
is a full list of the graffiti drawings.