The examine text for Lumberjack Leif (an NPC on Miscellania) is "He's a lumberjack and he's okay." Additionally, two woodcutting-related Tasks are titled "I'm a Lumberjack and I'm Okay" and "I Sleep All Night and I Work All Day".
If you speak with Bob the Cat while your own cat is with you, the two cats will re-enact the dialogue from the Luke, I Am Your Father scene in The Empire Strikes Back. Similarly, if you type "I am your father" into your in-game notepad, the note that shows up will instead say "Nooooooooo!"
Bork, the Big Ork, summons Ork Legions that spout Borg catchphrases like "Resistance is futile!" and "We are the collective!"
If you perform poorly in the Great Orb Project minigame, one of the wizards will comment that "This was a disaster! I'm making a note here: HUGE FAILURE." Additionally, the examine text for the portal that transports you between Runecrafting altars is "Look at you, examining things when there's Runecrafting to do." And in the "Meeting History" quest, the examine text for a portal is "There is cake in here, apparently."
The Fairy Godfather's henchmen Slim Louie and Fat Rocco both have examine texts that quote Goodfellas.
The monkey bars in the Brimhaven Agility Arena have examine text that quotes "I Wanna Be Like You", the monkey song from The Jungle Book. The pillars have the examine text "A small step for a player, a giant leap for player kind," a quote from Neil Armstrong, the first man on the moon. The poison darts have a Bullet Time dodge animation referencing The Matrix.
One of the smaller pigs in Draynor Village has the examine text "I shall call him...Mini-Pig." The same reference is duplicated in the examine text of the baby moles in the caves underneath Falador garden.
The "Zombie Dance" emote is one of the dance moves used in Michael Jackson's Thriller music video. The examine text of the Zombie Boots is "Thrilling!"
In Dungeoneering, you can get an award for being killed by a Bovimastyx dinosaur. If you do, you'll be treated to a Jurassic Park quote.
Edgar Allan Poe's short story "A Cask of Amontadillo" is about a wine connoisseur named Fortunato. The wine salesman in Draynor Village is named Fortunato; his examine text is "He looks as if he could do with a sip of Amontillado."
Naturally, the Raven pet's dialogue contains additional Edgar Allan Poe references.
If you give a cowbell to the penguin musicians Ping & Pong, they'll use it to play a song. Afterwards, they'll note that it needs more cowbell.
If you use the Ring of Charos to magically enhance your powers of persuasion, you can unlock "These Aren't the Coins You're Looking For" by convincing the sailors to give you a free ride to Karamja. There's also "TzHaar Wars" for playing a minigame in the TzHaar area.
Speaking of "A Clockwork Syringe", the final part of that quest is essentially a big shout-out to Bioshock. You have to infiltrate a facility disguised as what's essentially a Pirate Zombie Big Daddy, and just in case we didn't get it, the examine text for one of the enemies reads "Would you kindly kill these slicers?"
The Christmas 2011 Event has you gather ingredients for a bunch of goblin chiefs. You placed the ingredients in a cannon and it begins firing out of control. The goblins get hit, but your character dodges the shots by backflipping Matrix style.
Estocada, who gives out duellist's caps at the Duel Arena, has dialogue based on The Most Interesting Man in the World, including such lines as "I don't often replace hats, but when I do, I choose to replace duellist's caps." and "Stay victorious, my friend." As a bonus, his examine text quotes a line of Inigo Montoya's dialogue from The Princess Bride.
Zachory Bragg, of the Temple Trekking/Burgh de Rott Ramble minigame, has a personality loosely based on Zapp Brannigan of Futurama. His dialogue includes several Brannigan quotes, like "Be careful; this whole area is uncharted. But that might be because I lost the chart."
You can knock on a door in the west Varrock bank, and someone asks who's there. This is a setup for a knock-knock joke, and you're provided with three responses. One of them is "Doctor".
There's a mini game on Lunar Isle where you help a magical farmer to grow Triffids, er, Livids.
The fights in the Dominion Tower seem to pay tribute to Mortal Kombat. The health bars on the top of the screen, plus the inhumane voice narrating, adds to the Mortal Kombat theme. There's even a special fight named "Finish Him!".
Tuai Leit: "If a westerner has met a sea singer, soothsayer or siren, it was likely here; it is a minor centre of study and research for those not enamored of the civilized east." (Twilight Sparkle, the bookish unicorn devoted to her study of magic.)
Ai Jei: "One of the larger eastern islands. Produces gunpowder which is traded with the rest of the Wushanki Isles, and also grows apples. The ruling khan is territorial and hostile towards all westerners." (Applejack, who works on an apple farm.)
Rei Ti: "A mining colony originally built to dig for black slate; it has become highly prosperous since discovering large quantities of high-quality gems." (Rarity, a unicorn with a fondness for gemstones.)
Kei Pi: "The people of Kei Pi are renowned for their energy and hedonism, although some say that the vicious group of pirates known as the Pin operate out of a hidden base here." (Pinkie Pie, a hyperactive pony who loves to party.)
Flou Tar-Shei: "Officially accorded neutral ground, this island is a place of peace. Khans can relax here, if nowhere else." (Fluttershy, who is quiet and gentle.)
In the backstory of the Eastern Lands, you learn about someone named Quin trying to take over. The Dragon to Quin is someone named Discord, a character on the show.
There area a couple more references to FiM.
Brian O'Richard: The pressure will become dangerous in ten seconds flat so, if you don't leave in that time, the safety systems in the factory will remove you for your own good."
Kaqemeex: The trolls represent disorder. For us it is a major, immediate imbalance to the elements of harmony. But we need to call upon Guthix to right it with all haste.
In The World Wakes, at one point you need to assign different NPC allies to different fights, based on their strengths and weaknesses. One of the fights is against Zemouregal and his zombie army. The correct choice to fight them? The plant-like automatons led by Cres.
When you have the complete Maul of Omens in the boss fight against Vorago, the left click option is "Finish Him!"