Earthbound (SNES)

Cross-Series (Super Mario Bros.): The two lead singers of the Runaway Five look like Mario and Luigi. (Screenshot)
Status: Coincidence?: In the Japanese version of Earthbound (Mother 2), the entire band, including the lead singers, are wearing black. Only in the American version are they wearing red and green. My theory is that they weren't originally supposed to be based on Mario and Luigi, but someone noticed the resemblance while the game was being translated and had their colors changed.

Famous Person (The Blues Brothers): The Runaway Five (at least the lead singers) were inspired by the Blues Brothers. They were called the "Runaway Brothers" in the Japanese version, so this reference does appear to be 100% true after all.
Status: TRUE: Too similar to be coincidence, particularly the way they look as clay models that were pictured in the game's strategy guide. My second theory for the color change could be that Nintendo was paranoid about copyright infringement lawsuits. (But that's pure speculation.)

Cross-Series (Donkey Kong/Space Invaders): In the arcade, although it is pixelated greatly, you can see the original Donkey Kong and Space Invaders arcade games. (Credit: Bomberguy221)
Status: TRUE: (Screenshot) proves it.

Famous Person (Mr. T): There are NPC's in some towns that look like super-deformed versions of Mr. T. (Screenshot)
Status: Coincidence?: It could be coincidence, but they really do look like him.

Movie (War of the Worlds): The title screen of Earthbound is a scene from War of the Worlds. (Credit: Deathspork)
Status: TRUE: (Screenshot) proves it.

Music (Chuck Berry): The New Age Retro-Hippie's song is a derivation of a Chuck Berry song, either "Back in the USA" or "Johnny B Good". (Credit: Kairobi King)
Status: TRUE: (Midi) This song gets parodied in a lot of games. It also appears in City Connection and Final Fantasy Mystic Quest.

Famous Person (Nessie): Tessie, the dinosaur in the lake, is obviously named after (and based on) "Nessie", the not-so-infamous-anymore "dinosaur" of Loch Ness. (Screenshot) (Credit: James FP)
Status: TRUE: Verified by FO. Obvious reference.

Programmers: There is a dog in one of the towns named "Ruffini" who becomes "possessed" by the personality of one of the game's programmers. If you talk to him after beating the end boss, but before returning home, he'll give you an address to write to about your opinions of the game. (Credit: James FP)
Status: TRUE: Screenshots prove it: (Screenshot 1) (Screenshot 2)

Programmers: There is a sign in Fourside that mentions something about work on a project for the (now-illfated) Earthbound 64 (Screenshot). There is also another sign that mentions Hal Laboratory (one of the game's developers) and says that you can see Mt. Fuji from their location. (Screenshot). (Credit: James FP)
Status: TRUE: Verified by FO. Screenshots prove it.

Programmers: There's also a reference to APE, the other developer of Earthbound, in the form of a kid who wants to be one of their programmers when he grows up.
Status: TRUE: (Screenshot) proves it.

Movie (Rambo): One of the Sharks compares Ness to Rambo.
Status: TRUE: (Screenshot) proves it.

Real Place (Apollo Theater): "Topolla Theater" is possibly a take on "Apollo Theater". (Screenshot)
Status: TRUE: Names are too similar to be coincidence.

Famous Person (The Beatles): There are several references to the Beatles. One is a question about the song "Yesterday" (Screenshot), and the other is a Yellow Submarine (Screenshot).
Status: TRUE: Verified by FO. Screenshots prove it.

Console (NES): Ness was most likely named after the NES.
Status: TRUE: Verified by FO. I seriously doubt it's coincidence.

Cross-Series: (The Legend of Zelda: A Link to the Past) There is a sign in Twoson with a strangely similar message to that of a sign in the south part of Kakariko Village in The Legend of Zelda: A Link to the Past.
Status: TRUE: Screenshots prove it: (Earthbound Sign) (Zelda Sign) Also, both games were translated by Dan Owsen. Either he made a reference on purpose, or he was reusing dialogue.

Cross-Series (Super Mario Bros.): In the Japanese version of the game, some of the default character names were that of other Nintendo characters, such as Mario, Peach, Yoshi, and Kinopio (Toad).
Status: TRUE: Verified by FO. Source: Starmen.net.

Products (Coca-Cola): In the Japanese version of the game, the red trucks with the running stick figure on them were actually Coca-Cola trucks. (Screenshot)
Status: TRUE: Verified by FO. Source: Starmen.net.

Literature (Gulliver's Travels): The first two Sanctuary locations, Giant Step and the Lilliput Steps, are a reference to Gulliver's Travels. (Giant Step Pic) (Lilliput Steps Pic)
Status: TRUE: Verified by FO.

Commercials (Tombstone Pizza): There is a reference to those old Tombstone Pizza commercials that say, "What would you like on your Tombstone?"
Status: TRUE: (Screenshot) proves it.

Art (Salvador Dali): The Dali's Clock enemy is a reference to artist Salvador Dali and his famous melting clock paintings.
Status: TRUE: (Screenshot) proves it.

Famous Person (Thomas Jefferson): Though it's spelled the Spanish way, there's a reference to former president Thomas Jefferson. (Credit: Flying Omelette)
Status: TRUE: (Screenshot) proves it.

Literature (Casey at the Bat): The Casey Bat is named after the famous poem "Casey at the Bat" by Ernest Lawrence Thayer. In the poem, Casey struck out, and likewise, the Casey Bat misses its targets most of the time.
Status: TRUE: Verified by FO.

Earthworm Jim (Multiplatform)

Famous Person (David Bowie): Earthworm Jim's two different eyes are a David Bowie reference.
Status: TRUE: Someone from Shiny, the creators of the game, verified this in Nintendo Power.

Music (Mussorgsky): The second level ("What the Heck") uses Modest Mussorgsky's Night on Bald Mountain for the first half of its music. (Credit: Yashiro Nanakase)
Status: Unverified

Movie (Monty Python & the Holy Grail): The cow launching is a tribute to Monty Python and the Holy Grail. (Credit: Creature of War)
Status: Unverified

Programmer: The Andy Asteroid levels were named after the programmer Andy Astor. (Credit: Codie Martin)
Status: TRUE: Verified by FO.

TV Shows (Tex Avery): When Jim sees Princess What's-her-name, he does an impersonation of the wolf from the Tex Avery cartoons. (Credit: ShadOtterdan)
Status: TRUE: (VGmuseum.com) proves it.

Earthworm Jim 2 (Multiplatform)

Cross-Series (Mortal Kombat): In the first stage, "Anything but Tangerines", when you meet up with Bob the Fish, a message flashes on the screen saying "FINISH HIM!" in the same bloody slash letters used in Mortal Kombat. (Credit: Iqniz)
Status: TRUE: Verified by Crawl and 1000.

Music (Beethoven): The background music for when Jim is in the intestine level is Beethoven's Moonlight Sonata. Also, the music for the boss of the ISO 9000 level is the third part of Moonlight Sonata. (Credit: Crawl and 1000 & ShadOtterdan)
Status: TRUE: Verified by FO.

Movie (Lorenzo's Oil): The stage "Lorenzen's Soil" had its name taken from the movie "Lorenzo's Oil". (Credit: Codie Martin)
Status: TRUE: Verified by FO.

Ehrgeiz: God Bless the Ring (PS1)

Cross-Series (Final Fantasy 7): Cloud, Tifa, Sephiroth, Yuffie, Vincent, and Zack from FF7 are playable characters. And the boss Django is kinda like Red XIII. Also, in the Quest mode, some weapons from FF7 can be bought. Like Cloud's Buster Sword and Sephiroth's Masamune. (Credit: Ace Whatever)
Status: TRUE: Verified by FO.

Elemental Master (Genesis)

Cross-Series (Lagoon): Those one-eyed flying insects from Lagoon are in it. (Credit: Magical Yard Gnome)
Status: Unverified

Equinox (SNES)

Character Cameo: In the end, you rescue Shadax, the hero of Solstice. Yes, I know Equinox is the sequel, but I had to mention this anyway, because it's really bizarre that Shadax and Glendaal look nothing alike, and don't even look like they belong in the same time period or setting (one is an English Wizard, the other an Arabian Knight), yet they're supposed to be father and son!
Status: TRUE: (Screenshot) proves it.

Literature (The Silmarillion): In the Silmarillion, a Tolkien book, Melkor is described as the one god-turned-evil. Everyone hates him. "Melkor" sounds similar to "Melkior", which is the name Equinox gives to the wizard Shadax fought in Solstice, though he was called "Morbius" in Solstice. (Credit: Garland J. LaPalme)
Status: Unproven: It's hard to say if Melkior is truly a reference to Melkor, but if not, where did Equinox's designers get this name from? Solstice clearly calls that character Morbius.

Escape From Monkey Island (PC)

Real Place (Starbucks/Planet Hollywood): The "Starbuccaneer's" & "Planet Threepwood" shops on Jambalaya Island are parodies of real-life franchises Starbucks & Planet Hollywood, respectively. (Credit: SlyDante)
Status: Unverified

Cross-Series (Pokemon): One of the items you take from the school on Knuttin Atoll is a "Lechuckachu" card from the "Piratemon" card game. Sounds like a spoof of Pokemon. (Credit: SlyDante)
Status: Unverified

Eternal Darkness: Sanity's Requiem (GCN)

Literature (H.P. Lovecraft): The Ancients are based on H.P. Lovecraft's Great Old Ones; gods that once ruled the world that were sent into exile, and are now trying to take it back. (Credit: Codie Martin)
Status: TRUE: Verified by FO. Note: Much of Lovecraft's early work is in public domain, so that's why Silicon Knights could get away with using them.

Literature (Hamlet): One of the sanity effects causes your character's head to fall off. If you pick it up, the character starts reciting Hamlet. (Credit: Codie Martin)
Status: Unverified

Literature (The Rats in the Walls): The scenario with Maximillian Roivas is based on the H.P. Lovecraft story "The Rats in the Walls". (Credit: ShadOtterdan)
Status: Unverified

Literature (H.P. Lovecraft): The worms that attack Roberto, Edward, and Micheal are "Lovecraftian". Also, when Alex collects the page to Peter's chapter, you're taken to a cutscene with Pious bending over some human slicing things out of him with a hook-shaped dagger. According to Lovecraft, a sacrifice could be made more potent by removing certain organs. (Credit: Codie Martin)
Status: Unverified

E.T. The Extra-Terrestrial (Atari 2600)

Cross-Series (Raiders of the Lost Ark): You can turn the flower into the Yar from Yars Revenge and Indy from Atari 2600 Raiders of the Lost Ark. (Credit: Kairobi King)
Status: TRUE: Verified by FO.

Programmers: You can make Howard Scott Warshaw's initials appear and also "JD", which are the initials of the game's graphic designer. Also, the phone pieces are in the shape of the letters H, S, and W, which is the programmer, Howard Scott Warshaw's initials. (Credit: Kairobi King)
Status: TRUE: Verified by FO.

EVO: Search for Eden (SNES)

Movie (2001: A Space Odyssey): The Time Trans doors that appear between chapters are based on the large, shiny black rectangular monolith from the movie "2001: A Space Odyssey".
Status: TRUE: (Screenshot) proves it.

Excitebike 64 (N64)

Specific Reference: You can unlock the original NES Excitebike in this game. You can also unlock a 3D version of the original Excitebike later on. (Credit: Mark Kelly)
Status: TRUE: Verified by FO. Source: Nintendo Database.

Extra Innings (SNES)

Famous Person (Various): The players on one of the teams are all named after people who work for or used to work for Nintendo Power magazine, including Gail Tilden (editor-in-chief), George Sinfield (of "George & Rob"), and others. There is even a player named "Nester". Another team has players named after famous authors, like Kafka, Tolkien, and (James Fenimore) Cooper.
Status: TRUE: Verified by FO.

Famous Person (Various): I'm beginning to think that everyone in this game is named after someone famous. There are teams with people named after famous painters, authors, musicians, philosophers, scientists, mathemeticians, politicians, and more. A sampling of the names: Giger, Moebius, Poincare, Freud, Euclid, Aristotle, Achimedes, Copernicus, Galileo, Davinci, Brubeck, Coltrain, Bowie, Mozart, Gandhi, Kennedy, Dali, Picasso, Matisse, Mondrian, Warhol, Monet, Gogh, Gaugin, Rodin, Manet, Kipling, Wordsworth, Lennon, Marx, Castro. One team has the names, Crosby, Stills, Nash, and Young right in a row like that. Another has Deckard and Tyrell from Blade Runner and Page and Plant of Led Zeppelin. There is even a team with Founding Fathers Washington, Franklin, and Adams. And one team has so many famous scientists and people that I just decided to take screen captures of it rather than list them: (Screenshot 1) (Screenshot 2) (Credit: Crawl and 1000 & Flying Omelette)
Status: TRUE: Verified by FO.

Console (SNES): There is a really scary picture of a kid with a Super Famicom for a head on the select screen.
Status: TRUE: (Screenshot) proves it.