In Vilemyr Inn, Ivarstead, you'll find a woman by the name of Temba Wide-Arm. Her name is a subtle reference to the Star Trek: The Next Generation episode 'Darkmok', in which Picard and his crew encounter a race of aliens called the 'Tamaraians'. At one point, Picard is stuck on a planet's surface. He attempts to make a fire, but fails. A Tamarian named Dathon takes a branch from his own fire and throws it to Picard, saying "Temba, his arms wide", to make it clear the fire was a gift.

Just south of the shrine to Peryite, you can find a skeleton about halfway up the mountain. If you look just to the side of the skeleton you will see a sabre cat stuck between two rocks with a weapon lodged in its head. This is a reference to a scene in the movie "300" where Leonidas leads a wolf to a narrow passage, and then stabs it in the head with a spear.

During the quest "Proving Honor", if the Dragonborn asks Farkas if the companions are werewolves, he ends his response with "It's a secret to everybody." This is a reference to The Legend of Zelda series, where this phrase is infamously repeated.

Directly south of Markarth, near Purewater Run, there is a stone bridge near a waterfall. If it's your first time there, you'll see two goats walking on the bridge, and then a third one climbing up from under the bridge to join them. If you go under the bridge you can find a dead troll. This scenario is a reference to the Norwegian fairy tale "Three Billy Goats Gruff".

When near Sheogorath, he will sometimes say "Do you mind? I'm doing the fishstick. It's a delicate state of mind." This is a reference to the Fishy Stick meme which began on Bethesda's Official Forums and went on to become a running gag in Elder Scrolls games.

When Athis is asked why he joined the Companions, his response is "Fortune and glory, friend. Fortune and glory." This is a reference to a very similar line from Indiana Jones and the Temple of Doom.

During the night, you may encounter a Headless Horseman, a reference to Washington Irving's "The Legend of Sleepy Hollow".

The guards in Skyrim will more often than not say "Let me guess, somebody stole your sweetroll" to the player, this is a gag that Bethesda Softworks have been running since the very first Elder Scrolls game.

It's possible that the popular phrase, "I used to be an adventurer like you, until I took an arrow in the knee" was put into the game because Skyrim was the first Elder Scrolls game to not include greaves (knee armor).

The DLC Expansion for Skyrim, "Dragonborn", contains many of the music tracks that were previously found in The Elder Scrolls III: Morrowind. This is fitting, seeing as the game is set on the island of Solstheim, in close proximity to the Morrowind region of Tamriel.

The Dragonborn DLC contains a reference to Morrowind in which a Wizard casts a spell attempting to fly but winds up ultimately falling to his death.

Slightly Northeast of Bleakwind Basin, there is a pond with a skeletal arm holding a leveled sword, which is a reference to the Lady in the Lake in the legend of King Arthur.

In Endon's House in Markarth, there is a shelf in the back of the room with Sliced Goat Cheese, a row of Garlic, and some Glow Dust arranged to look like a scene from Pac-Man.

At the very top of the Throat of the World, there is a special pickaxe that the player can obtain. The name of this pickaxe is 'Notched pickaxe', and is thought to be a reference to Minecraft creator Notch.

Southwest of Winterhold, in Bleakcoast Cave, there is a part of the cave guarded by frost trolls where you will find parts of a skeleton hanging from the icy ceiling. On the ground below it is a Steel Greatsword of Weariness. This is a reference to Star Wars: The Empire Strikes Back in which there is a scene where Luke Skywalker is stuck to the ceiling of an icy wampa cave and must use the Force to retrieve his lightsaber to cut himself free.

Charles Martinet, voice actor of several main characters from the Mario series, voices Paarthunax, a dragon.

In the games files there is an unused Pit or Arena Called "Windhelm Pit Entrance". Entering the Pit spawns 2 Argonians (Both Male), Nords, Dark Elves and Imperials NPCs, They are all called 'Pit Fans', who are supposed to be spectators. It is believed that Windhelm was going to have an arena at some point of development where you would face against animals or NPC Bandits. There are also Pit guards who are fully voiced, but they cannot be viewed during normal gameplay. The place can be viewed by entering the console commands "coc WindhelmPitEntrance" and "coc WindhelmPitExterior".

The leader of the Thieves Guild, Mercer Frey, has the same voice actor as another well known thief, Garrett from the Thief series. Both are voiced by Stephen Russell.

In the Heroic Fantasy book 'The Name of The Wind' by Patrick Rothfuss, the main character Kvothe stumbles at one point (Page 22 in the attached PDF) and says "I took an arrow in the knee on my way through the Eld three summers ago" The book was published in 2007 and might be where Bethesda got the line from. If this is the case, then 'arrow in the knee' may be an Easter egg or reference to the novel.

The quest "Mind of Madness" has parallels with the story "Alice in Wonderland", where Alice is instructed by The Mad Hatter to do several menial tasks while he has a tea party. When you do finish the quest, you get the staff of "Wabbajack", a reference to the poem "Jabberwocky".