The theme of the Scramble for Africa scenario, "Ujuba na Takaburi," has its lyrics taken from a Swahili poem written during the European and Arab colonization of Africa. The poem itself is protesting against the Arab rule at the time.

Three unused World Wonders exist in the game's data. These are the Large Hadron Collider, which only has a completion theme and placeholder image, the Panama Canal, which only has an icon and completion image, and the Three Gorges Dam, which has an icon, image, and unused space for a completion theme.
Several unused "new technology discovered" voice clips can be found within the game's data. These include files for Calculus, Patronage, Publishing, and an early quote for Ballistics.
The 37th city on America's list of names is Hunt Valley, Maryland, the current home of Sid Meier.
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The achievement for researching Horseback Riding as Russia before all other civilizations do the same is named "My Little Pony". This is both a pun on the popular Hasbro toy brand of the same name, as well as a subtle nod to the many myths of Catherine II's sexual affinity for horses.
The achievement for getting a Space Victory as Casimir III, "Poland Can into Space", is a reference to the internet meme cartoon Polandball and its recurring joke that "Poland cannot into space"
Attila the Hun speaks in modern Chuvash, the closest surviving language to Hunnic speech, yet his voice actor is not a native speaker of Chuvash, making several grammatical, diction, and pronunciation errors in his speech.

In the background of Gustavus Adolphus' diplomacy screen is a portrait of Eric XIV, one of the kings of Sweden prior to Gustavus' reign.

In George Washington's diplomacy screen, a painting of the Oracle's completion art can be seen above the fireplace.
While most leaders speak in the language of their homeland, Ramesses II speaks in Fusha (an Egyptian accent of Arabic) instead of Ancient Egyptian. This was likely chosen because the closest possible language, Coptic, has very few speakers, and because pronunciation guides for Ancient Egyptian hieroglyphs were never recorded.

Singer T-Pain and two members of the comedy group The Lonely Island can be seen in the bottom right corner of the picture that appears when the player builds The Sydney Opera House. This is a reference to the music video for "I'm on a Boat".
The XCOM Squad is a reference to the videogame XCOM: Enemy Unknown, which was also developed by Firaxis.
The unit image displays soldiers carrying the Heavy Plasma weapon. This is an energy-based weapon and does not fire projectiles. This weapon defends these soldiers in place of guns that leave behind metal slugs which would potentially rupture the hulls of space craft. Their armor is loosely based on the Titan Armour. Interestingly, the armour required extensive research of alien technology, and the weapon itself was created and designed by the aliens in question - despite there being no such alien invasion in the Civilization world (yet).
The unit image displays soldiers carrying the Heavy Plasma weapon. This is an energy-based weapon and does not fire projectiles. This weapon defends these soldiers in place of guns that leave behind metal slugs which would potentially rupture the hulls of space craft. Their armor is loosely based on the Titan Armour. Interestingly, the armour required extensive research of alien technology, and the weapon itself was created and designed by the aliens in question - despite there being no such alien invasion in the Civilization world (yet).