- One cookie milestone in particular is a reference to the Milkshake song by Kelis:
"Your cookies brings all the boys to the yard."
- The Grandma icon◊ and another status update quote is referencing an image macro meme◊ based on the movie The Master of Disguise:
- The "Ultimadrill" upgrade's accompanying quote is a reference to Tengen Toppa Gurren Lagann:
"Pierce the heavens, etc."
"Do the impossible, see the invisible. Roe roe, fight the power?"
- As is the Salmon Roe egg.
- The "Flux Capacitors" Time Machine upgrade is a pretty obvious reference to Bake To The Future... Er, Back to the Future.
- One upgrade for the portals is called "Sanity dance":
'We can change if we want to. we can leave our brains behind.'
- One of the achievements is titled "Quantum Conundrum".
- The achievement for building 1 portal is "A whole new world", referencing the song from Aladdin.
- Achievement for building 50 portals is "Now you're thinking."
- The achievement for having 100 cursors is "Of Mice and Men", a reference to the Steinbeck novel of the same name.
- The achievement for having 100 alchemy labs is "Gold Member", referencing the third Austin Powers movie.
- The quote on the "Nihilism" achievement: "There are many things that need to be erased."
- The description for the "Get Lucky" achievement references Daft Punk's song "Get Lucky":
"You've been up all night, didn't you?"
- The Flavor Text for the Quintillion Fingers upgrade is a direct quote from Boomhauer. It gets pretty hilarious if you remember the context of the original quote; you probably know why the hands are so effective now.
Yeah man, I tell ya what, man, that dang ol' internet, man, you just go in on there and point and click, talk about w-w-dot-w-com, mean you got nekkid chicks on there, man, just go click, click, click, click, click, its real easy, man.
- The Kitten Workers upgrade has the Flavor Text "meow meow meow meow," a probable reference to the four-descending-notes Ear Worm jingle of "Meow Mix" cat food.
- I'll say one word, just one: "cookies".
- One Time Machine upgrade is called "Time Paradox Resolver" and the description states: "No more fooling around with your own grandmother!". Squick!
- Several from the Halloween cookies:
- Bat Cookie: "The cookies this town deserves."
- Eyeball Cookie: "When you stare into the cookie, the cookie stares back at you."
- Spider Cookie: "You found the recipe on the web. They do whatever a cookie can."
- The 'Chocolate Monolith' upgrade for interplanetary shipping: "My god, it's full of chocolate bars!"
- The final Santa upgrade: "My name is Claus, king of kings; look on my toys, ye Mighty, and despair!"
- From the Christmas Cookies:
- The Festive Hat upgrade: "Not a creature was stirring, not even a mouse."
- The last line of the Heavenly Chip Secret flavor text is "It's a secret to everyone", a reference to The Legend of Zelda I
- The Jaffa Cake cookie upgrade makes reference to the Yogscast Tekkit series, Jaffa Factory.
"If you want to bake a cookie from scratch, you must first build a factory."
- The Flavor Text for the first Prism upgrade, "Gem Polish," concludes with "Truly, truly outrageous."
- The achievement for having 150 Shipments is "Type II civilization," a reference to the Kardashev scale.
- As of Version 1.0417, the Mine-related achievement "Never dig down" is a reference to one of the things you shouldn't do in Minecraft.
- The achievement for making 1 septillion cookies just from prisms is called "Praise the sun".
- The achievement for having 250 grandmas is "The old never bothered me anyway".
- The eclipse cookie's flavor text "look to the cookie" comes from Seinfeld, where Jerry appeals to Elaine to see a half-black, half-white cookie as a metaphor for racial harmony.
- The Duck Egg upgrade of the easter season has the flavour text ''Then he waddled away."
- The "Wishalloy Mouse" upgrade references the band Smash Mouth and the lyrics of their song "All Star".
"Clicking is fine and dandy, but don't smash your mouse over it. Get your game on. Go play."
- The Easter grandma skin is a grandma wearing a stupid bunny suit.
- The achievement Realm of the Mad God is a shout out to the videogame of the same name.
- The Bunny Biscuit upgrade has a reference to Watership Down. The icon also looks like The Black Rabbit of the film version, although obviously much more cheery.
"All the world will be your enemy, and when they catch you they will kill you... but first they must catch you."
- The achievement for buying 400 cursors is "Dr. T."
- The 350 grandma achievement is "To Oldly Go."
- The 300 temple achievement is "Wololo," from the sound priests would make when trying to convert enemies in Age of Empires.
- The achievement for baking 100 octillion cookies is "He who controls the cookies controls the universe" The milk must flow.
- The achievement for baking 1 quadrillion cookies a second is "Turbopuns" with the description "Mother Nature will be like slowwwww dowwwwwwn."