Portal (series)/Shout-Out

Portal

The ending song jokingly and mockingly references Black Mesa. Songwriter Jonathan Coulton also namedrops another of his popular songs, "I Feel Fantastic".
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.

Portal 2

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 turrets were 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 opening credits.
A Dummied Out line from co-op mode's original plot involving GLaDOS trying to get Atlas and P-Body to behave more like humans involved them bringing back a comic strip about a cat who freeloads in a man's house and eats all his lasagna. She's not very impressed, and decides to rework it.
One of the Achievements is called "Narbacular Drop", a shout out to the student project that eventually became Portal.
The Bots trailer features Atlas holding a frying pan with a pancake. A bit of a Take That with Atlas just not doing it right.
One of the Fact Core's facts is "In 1948, at the request of a dying boy, baseball legend Babe Ruth ate seventy-five hot dogs, then died of hot dog poisoning."
In the comic, Chell's file states her test subject number as 1498, as well as a certain imprisoned mangaka.
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 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.
One of the co-op achievements is called "Can't Touch This"
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.
When navigating through the manufacturing factory with Wheatley, he off-handedly starts telling a ghost story. "They say the old caretaker of this place went absolutely crazy, and chopped up his entire staff...of robots."
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."
From the Peer Review DLC: "Ahem, if you can dream it, you can-- oh for god's sake..."
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 is a reference to the dance the Wizzrobe from LoZ: Majora's Mask preforms before attacking Link.

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, JK Simmons, appears in a series of commercials for Farmers Insurance as a professor at the fictitious "University of Farmers".
One of the parallel Caves mentions Soylent Green.

Cave: Memo says Soylent Green is...let's see...doubling in price. Now, I don't care how good people tastes, it's costing us more than lobster so we're all going back to fish-sticks.

Another parallel's apparently working on the world's first half-man, half-machine police officer, Roboticop.
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.
And in yet another Cave complains about magic sunglasses that let the wearer see subliminal messages on the walls.
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.