Halloweentown: Threed. Ghoasts, zombies, dim light, spooooky puppets... Even after you take care of those problems the color scheme is still muted and there is still a huge graveyard.
The Heartless: Many of the enemies in the game are influenced to fight Ness through Giygas's control over their inherent evil. Right before Ness gets charged with a great deal of power, he has to fight Giygas's influence over the evil in his mind via a boss battle.
Heel-Face Revolving Door: Pokey seems to like trying to pretend he's ready to repent of his misdeeds for just long enough to make a getaway. And boy, does he ever run fast for a little fat kid.
Hell Hotel: The hotel in Threed will briefly become this as soon as you get there.
Heroic Mime: Whoever the player is controlling at the time. As soon as they meet up with the main group, they start talking and introduce themselves. The only exception is at two points in the game, where a special wall displays Ness' thoughts, and where Ness talks to himself telling him where he needs to go next near the end of the game.
Hope Spot: During Ness' visit in Magicant, Pokey is seemingly determined to make peace with him despite enough tension between them throughout half the adventure. Then the endgame comes and everything is suddenly ruined.
Instant Awesome, Just Add Dragons: The bag of dragonite, which turns the player into a dragon temporarily, has no explanation where it comes from or how it is made. Although a monkey wonders, "is it really made by dragons?"
Parodied - at one point your path is blocked by a statue of a pencil. In the original Japanese, it was of an octopus.
Later on is another parody, where the blockade is an eraser statue. Originally, it was a statue of a type of doll (the item to remove it forms a play on words in Japanese). The English versionretains that sort of pun—the pencil statues are removed using a Pencil Eraser. No prizes for guessing what removes the eraser statue.
Also, if any player character gets mushroomized, the game's interpretation of D-pad inputs will rotate 90 degrees clockwise every thirty seconds. This can only be cured by the healer in the hospital, and you will have a hard time getting there.
Item Amplifier: Using the right condiment with the appropriate food increases the healing power of the latter.
Jerk with a Heart of Gold: Everdred, boss of Burglin Park. Apparently he is some sort of criminal, and he does briefly fight you, but after that he is nothing but helpful. And he really wanted Paula to be rescued.
Joke Character: The worthless protoplasm, fobbies, and foppies are joke enemies, and Pokey amounts to a joke ally for the short time he travels with you.
Parodied, when the protagonist Ness can get items from trash cans. And this includes food items, which he can then eat with absolutely no consequences. He also gets the chance to properly steal food items, but will be attacked for it.
There is also an NPC (in Summers, if memory serves) that lampshades the use of this trope in "other" games.
In a case of Video Game Cruelty Potential Jeff can steal the cookies for a kid's Birthday coming up the next day, the person who made them even says he made them all himself and frosted them with extra care. Though talk to him after you steal them, he gives a What the Hell, Hero?
The Runaway Five, Pokey, and Paula all have theme music - the latter's doesn't play all that often, though.
Paula's theme is actually a Shout-Out of the theme of Youngtown, a place where only children live because all of the parents were abducted by Giygas. So it's saying that she's tied down to a place with no adults to guide her and she's scared, helpless. Its only major appearance was in Paula's cell. Get why now?
Leaning on the Fourth Wall: During the brief period where the player directly controls Jeff, he saves his game by calling Maxwell. Maxwell notes that he'll make a record of Jeff's progress, and notes it's like saving in a video game.
Live Item: Keeping an egg in your inventory will eventually hatch it into a chick, which can provide a bit of relief from Ness' recurring homesickness. This stops once it grows into a chicken, which can then be sold for some cash.
As is commonly known by now, thanks to the MOTHER 3 fan translation and Super Smash Bros. Brawl, Pokey Minch's name in the original MOTHER 2 was Porky Minch. Many fans have reached the compromise solution (as seen here, on MOTHER 3 fan translator Clyde "Tomato" Mandelinnote who, despite making the decision to use "Porky" instead of "Pokey" in his MOTHER 3 translation, still calls him Pokey all the time's EarthBound website) to call him "Pokey" when referring to EarthBound, and "Porky" when referring to anything else.
The Apple of Enlightenment, mentioned several times throughout the game, is revealed towards the end to be a future-telling machine used by the evil forces. In the English translation, this line is removed, and as a result fans speculated for years about what the Apple was meant to be.
Also, Pokey's motive. After rescuing Paula the first time, Pokey says "Let's be friends again. Just kidding!" and is pretty much the bad guy for the rest of the game and the next game. In the original Japanese version, it wasn't because Pokey was a jerk, but because Ness was. Pokey asked Ness if they could be friends again, but Ness refused to answer, causing Pokey to storm off angrily.
Lost World: Aptly named the Lost Underworld, an enormous underground cave filled to the brim with bloodthirsty dinosaurs. Not to mention that your party's sprites minimized just to compare the sizes of your enemies.
Lucky Translation: A sign in Threed advertising a hint shop features a pun based on the cry of a horse that works in both English and Japanese.
Magic Meteor: The meteor that starts Ness' adventure. Not only was the time traveler Buzz Buzz riding in it, but the meteor contains a material needed for time travel.
Magic Is Rare; Health Is Cheap: PP-restoring items are hard to come by, especially in the early game. If you want the best of them, the Magic Truffle, be prepared to root through the Deep Darkness with the Piggy Nose for a long time (and there are only so many). Late game, however, you can buy the (mediocre) Magic Tart and the (better, especially for Poo) Brain Food Lunch.
Malt Shop: The burger stops you see throughout your adventure have this kind of style implemented.
Money Spider: Averted. As with the previous game, money is not dropped by monsters, but is instead received through transactions with your father. However, enemies will still drop... odd items at times.
Mood Whiplash: One of the most memorable examples in gaming. It's nowhere near as sudden as many assume and there's a good deal of buildup to it, but it's there.
Musical Pastiche and Sampling: It's used so frequently that the resulting legal muck is the most common theory behind why this game would not see an international re-release until 2013!This video shows the nearly insane amount of sampling that's gone into the soundtrack. It's amazing how being a small unheard-of RPG that's a commercial disaster in the USA allows this sort of Getting Unlicensed Sampling Past the Radar. Most notably:
The almost surely lawsuit-inducing BeatlesSuspiciously Similar Song version (the Saturn Valley music is supposedly inspired by "Wild Honey Pie", the "waking up in a hotel theme" starts with a short quote from "Good Morning, Good Morning", and the shop theme resembles "When I'm Sixty-Four") and samples (the Dungeon Man theme samples the beats from "Sgt. Pepper's Lonely Hearts Club Band (Reprise)", entering Giygas' lair gives a short sample from the opening Marseillaise bit of "All You Need Is Love").
The "Sky Runner" theme uncomfortably resembling the opening synth from The Who's "Won't Get Fooled Again", one of the battle themes being an outright rip from The Champs' 1956 hit "Tequila", the naming screen theme using a short sample from the Monty Python's Flying Circus theme, "Moonside Swing" sampling from Ric Ocasek's song "Keep On Laughing".
The Monty Python's Flying Circus theme is actually "The Liberty Bell March" by John Philip Sousa, and is considered a public domain song. This means it's not covered by copyright.
The Sky Runner theme gets a special mention in that, according to this, it and the "Johnny B. Goode" soundalikes are the only things on the soundtrack that are considered a little bit too risky on the copyright side of things for the game to get rereleased (the one problem not pertaining to the soundtrack is the painting mentioned below). Considering just how much sampling and general musical grey area this game is dabbling in, it's quite amazing.
The Jackie's Cafe song sampling the Our Gang theme and interpolating "The Star-Spangled Banner"
The Runaway Five's final performance resembling The Doors' "The Changeling". The Chaos Theater's music overlaps between this and Suspiciously Similar Song by being very, very similar to the bass and guitar portions of "Cars Hiss by My Window" by the same band.
One of the most widely-remembered ones is the passing resemblance the Frank / New-Age Retro Hippie theme bears to Chuck Berry's "Johnny B. Goode", but they're not even close to identical as so many assume
The Cave of the Past is made entirely out of manipulating the opening to The Beach Boys' Diedre.