The game contains a secret talking mudcrab tucked away on a small island just to the east of Mzahnch in the Azura's Coast region, who's also the richest trader in the game.

M'Aiq the Liar is a Khajiit rogue who can be found on a small island southeast of Dagon Fel in the Sheogorad Region. He is an Easter egg, and much of his dialogue refers to many requested or anticipated features of Morrowind which were not included in the final release of the game. He also mentions another easter egg, the Mudcrab Merchant. He is encountered again in Oblivion and Skyrim with similarly-themed dialogue.

You can find a room called 'Kefka's Burial' in the dungeon Urshilaku Burial Caverns. This is a reference to Kefka Palazzo, the main antagonist in Final Fantasy VI.

The body of Indiana Jones can be found in a dungeon called Omalen Ancestral Tomb. Apparently a rock fell on his leg, dooming him to a slow death. There's a scroll that records his last thoughts, signed "Indie". It also mentions that his father made jokes about his childhood pet. In the movie The Last Crusade, Indiana's father exclaims at the mention of Indiana's name: "We named the dog Indiana!" This would be the childhood pet the scroll mentions.

Three locations visited during the main quest line have sections named after different Pokemon. The Illunibi Caverns have "Marowak's Spine", Arkngthand has "Weepingbell Hall", and the Urshilaku Burial Chambers have "Kakuna Burial".

On Azura's Coast, you can find a dead Redguard NPC called "Arlowe." On his body is a unique weapon called the "BanHammer." This is a reference to Richard "Lowtax" Kyanka, site creator of Something Awful, who was sometimes referred to as "R-Low" on the forums. The "BanHammer" was a common euphemism for someone getting banned from the forums.

The reference goes further in the Tribunal expansion. If you have the Mace of Slurring and go to Mournholds Museum of Artifacts, ask curator about the artifact and she will tell you, "It was crafted near the end of the Second Age by Kyanka, a slightly deranged Altmer weaponsmith and enchanter. He had a rather warped sense of humor, and apparently delighted at the thought of reducing opponents to a gibbering mess before crushing them to death."

The in-game book "The Egg of Time" depicts a Dwarven figure in an image inspired by Leonardo Da Vinci's Vitruvian Man.

There are three unique ashes in Morrowind:
Ashes of G. Lyngas, located in Ravel Ancestral Tomb.
Ashes of Lord Brinne, located in Samarys Ancestral Tomb.
Ashes of D. Bryant, located in Falas Ancestral Tomb.
These three are all dedicated to former regulars at The Elder Scrolls Forums, all of whom passed away during production.

In a cavern called Mudan Grotto there's a skeleton with the name "Peke Utchoo", which sounds quite similar to the Pokémon Pikachu. Whoever put the skeleton in also included a note that reads, "If anyone shall ever find me, I hope I am able to bring them to laughter." The note was probably put in to make sure that the player realizes that the skeleton is meant to be a joke.

North from Seyda Neen, there is an unique encounter in which a Bosmer wizard named Tarhiel will fall from the sky and crash in front of the player, dying from the impact. He holds three Scrolls of Icarian Flight, which temporarily boost the Acrobatics skill by 1000 points, for just 7 seconds. His journal, which mentions him testing them out as an experiment, lies next to his body.

"Icarian" refers to the greek mythological figure Icarus, who shared a similar fate. Whereas Icarus flew too close to the sun and fell as a result, Tarhiel forgot to take the landing from great heights into account. It is, however, possible to save him by casting a large-area Slowfall spell, but his only dialogue is "I don't want to talk about it", suggesting he is too embarrassed by his failure.

The name "Tarhiel" is also a reference, to the University of North Carolina Tar Heels, and his game id (agronian guy) refers to North Carolina's top Agronomy program.

A large number of names for the Ashlander NPCs, Egg Mines, caves/tombs and Daedric shrines in Morrowind are inspired by real-world ancient Assyrian and Babylonian names.

•Ahhe (used for the Asha-Ahhe Eggmine, the Ashlander NPC Ashu-Ahhe, the caves of Dun-Ahhe and Tin-Ahhe, etc) is a component of the names of Assyrian and Babylonian kings, such as Ashur-nadin-ahhe and Marduk-nadin-ahhe.

•Ashur-Dan (used for the Ashlander NPC Ashur-Dan, the fire-river Foyada Ashur-Dan and the cave Ashir-Dan) is the name for three Assyrian Kings.

•-ipal (used for some Daedric shrines like Assurdirapal and Zergonipal, and Ashlander NPCs such as Dunsalipal Dun-Ahhe and Shipal Zansatanit, etc) is a component for the Assyrian king Ashurbanipal.

•Ashur/Assur (forementioned in previous examples and more) is the Akkadian name for the Assyrian Empire and it's capital, Ashur/Asser. It's worth mentioning "Ashur" has a resemblence to "Ashlander."

•eriba- (Used loosely for the Erabenimsun Tribe) is a root for some Assyrian/Babylonian names (Eriba-Marduk, Sin-ahhe-eriba, etc)

•-nammu and -nummu (used for various caves/tombs and a few NPCs) is based off of a Babylonian King named Ur-Nammu.

•Sargon (used for the cave named Sargon) is the name of the founder of the Assyrian Empire (Sharru-kin, also known as "Sargon of Akkad.")

Other Ashlander names draw from other real-life cultures/people, such as Mamaea/Maesa who were family of the Roman emperor Elagabalus in the 3rd century (Julia Maesa was his maternal aunt and Julia Avita Mamaea was her daughter.)

In the in-game book called "No-h's Picture Book of Wood", it states that the last page of the book has the words "Boat Ack" scrawled about the margin in a vandalistic manner. This is a reference to the late Kurt Cobain, as in his teen years he enraged a neighbor by vandalizing a boat by painting the words "Boat Ack" on the side of it. The in-game book itself is rare and is found in only two locations, with one of them being on a boat called "Falvillo's Endeavor", which is docked near Vos.

In Jobasha's Rare Books, located in the Lower Waistworks of the Foreign Quarter in Vivec, there is a potted plant that has actually been named "Charles the Plant". The plant also holds an alchemy ingredient called Meteor Slime. This is a reference to two plants from Maniac Mansion, the first being "Chuck the Plant" who also appears in various other LucasArts games, and the second being the man-eating plant that the player can feed a meteor to.

Southwest of the Skaal Village and south-east of Castle Karstaag on Solstheim is Bjorn cave. Inside is a skeleton hanging by its feet from the ceiling with a sword stuck in the ice below it. This is a reference to Star Wars: Episode V - The Empire Strikes Back, in which Luke Skywalker is knocked out and captured by a wampa on Hoth. When he awakens several hours later, he finds himself hanging by his feet from the ceiling with his lightsaber in the snow below him.

Morrowind's data files contain a number of test rooms that can be accessed using the game console. The rooms include "Character Stuff Wonderland", "Clutter Warehouse - Everything Must Go!", "Draugr Test" (in BloodMoon), "ken's test hole", "Mark's Script Testing Cell" (in BloodMoon), "Mark's Vampire Test Cell", "Redoran Test", "Redoran Test 2", and "ToddTest".

Many of these rooms have self-explanatory purposes, although a few have noteworthy attractions in them. The "Clutter Warehouse - Everything Must Go!" room has two strange NPCs in it: Lord Cluttermonkey, who is an Argonian in Daedric armor who has a mace called Clutterbane, and the Used Clutter Salesman, a Bosmer dressed in exquisite clothes who has a Daedric warhammer.

There is a mounted head of an Argonian called "The Head of Scourge" in the basement storeroom of the Lizard's Head cornerclub in Vivec. This is a reference to Scourge, the character Bethesda developer Steve Meister (AKA MrSmileyFaceDude) used to test the game. Scourge was also the character Meister used to role-play on the Official Forums.

According to an interview, he discovered the head while testing the game and exploring Vivec. Since his character shared the same head model, he asked one of the developers to change the item name to match his character's.

It is possible to talk to Ash Slaves like normal NPCs if the player manages to interact with them without being detected first. When not trying to kill the Nerevarine, the Ash Slaves appear to be quite preoccupied with the arrangement of their furniture. In fact, their dialogue seems to imply that the furniture is talking to them and that they simply want it to be quiet. This explains why the furniture in Sixth House bases is always arranged in bizarre ways.

North of Vivec City is the Gro-Bagrat Plantation, where an Orc named Gakkenfeld has the only muffin in the game. Sadly, the muffin has no unique effects and has the same properties as bread.

Inside of the Sixth House base Hassour (south of Balmora) is a musical instrument called a "fat lute". This is a play on the term "phat lewt", which is Internet slang meaning powerful loot, typically used in MMORPGS.

There are three unused sound files named "moan2.mp3," "roar2.mp3," and "scrm2.mp3" that can be found in the Morrowind data files. These are placeholder sound clips of kittens that the developers used for the Kagouti while the game was still in development. The clips were obviously replaced with more appropriate noises for the Kagouti, but the files themselves were not removed.