The Dept. Store Spook in Fourside goes out of his way to avoid pronouncing "hell":
You will be gone, and you'll be burning in... Well, you'll go to heaven!
Never Trust a Trailer: Probably one of the most severe cases; the ads tried to make it look like a Grossout Game from beginning to end....note The slogan for the game is "This Game Stinks", for an example. There's maybe two parts of the game with any kind of Toilet Humor, and even then it's never too over-the-top.
Nice Job Breaking It, Herod: Giygas receives a prediction of his defeat and begins his invasion early in an attempt to reverse this. This likely would've worked, except that Ness is visited by an alien bee from the future and the two events end up canceling out.
Nintendo Hard: Much easier than its prequel, but still fairly frustrating nonetheless, particularly during the early game and during the Zombie part of Threed.
Non Standard Skill Learning: Spells are acquired by leveling up, except for the two tiers of Teleport for Ness. The first Teleport must be learned from a talking monkey, and the second one is automatically acquired after completing the Magicant level.
Only the American guide says he's 13. Although that is a reasonable age (since he is supposed to be the same age as Jeff, who is in boarding school and has been separated from his father for around ten years), it's not actually his official one.
Ominous Message from the Future: The events of the game are set in motion when Buzz Buzz comes from the future to warn Ness that Giygas has destroyed the world in the future and that a boy named Ness would defeat him.
Outside-the-Box Tactic: Continuing the series-wide trend, the Final Boss, Master Giygas cannot be defeated via normal tactics. You must use Paula's Pray command ten times before you, the player, defeat him.
The Overworld: The Eagleland overworld, which actually has roads, just like in Real Life! You sometimes get to ride in the tour bus with a local band down them, but otherwise you walk like in other RPGs.
Palette Swap: Several enemies are like this, including a stronger version of the Territorial Oak, Foppies and Fobbies, and the Mani Mani Statue/Ness's Nightmare.
Parental Abandonment: Ness' father communicates over the phone often enough, but is never home. Jeff's father hasn't seen him in ten years despite living fairly near his boarding school (and this is a twelve to fourteen year old boy) and seems to think nothing of it; his mother is never mentioned. Poo's parents are nowhere in sight—affairs of state, perhaps? Paula is the only one of the four protagonists to have parents that are both alive and present.
Parental Bonus: Oh God. Too many to list. A yellow submarine, the Runaway Five, the New Age Retro Hippie's battle music...
The Password Is Always Swordfish: The one password was not of the "easily guessed" type, but was ridiculous nonetheless: It consisted of waiting three minutes. Who would guess that?
This is later subverted by another character asking for the password. As the Player Character does not answer, he (or it) attacks ("someone so quiet is either extremely shy, or extremely dangerous").
Police Brutality: When Onett's police force is asked by a little boy to remove a roadblock and help him get to the next town, they decide it'd be fun to take him to the back room of the station and beat him up. They quickly learn challenging Ness to a fight is a bad idea if you don't want your butt kicked.
The first four towns are called Onett, Twoson, Threed, and Fourside.
And what are those numbers added up? NinTendo! Although that might not have been intentional.
And then there's Summers and Tenda (possibly also a pun on "tender"). Think about that for a while.
The main character, named after the NES. Alternately, the main character's name is an anagram of the system he first appeared on (SNES).
The bicycle shop in Twoson is called "Punk-Sure".
One removed from the American version: the third town was originally named Threek, combining both the numerical theme along with a scream of surprise and alarm. Perfect for a haunted town. Nintendo had it changed to "Threed" out of fears that it could be read as a reference to the KKK.
Random Drop: The infamous 1/128 items are this. The list of enemies that dropped items at a 1/128 rate in this game is huge, and most of those enemies dropped arguably worthless items. Some enemies that dropped valuable equipment at this rate had methods of expending your time...
Retraux: Giygas and Heavily Armed Pokey's battle theme starts out with some NESchiptune-sounding music (ironically, nothing from Earthbound Zero, though, where Giygas actually just had an incessant screech as his "battle theme") before spontaneously jumping into a rock version of the same tune.
The song that plays inside the Minch household would also count.
Sinister Geometry: Giygas's robots appear in the overworld as blue octahedrons (presumably they're inside; there's an unused capsule sprite that might have been originally used, same as the Starman capsules from MOTHER 1).
Giygas' stronghold, the Cave of the Past, is a chrome wasteland of of geometric cliffs.
Skippable Boss: Many players don't even realize they can just not fight Everdred.
Snowy Screen of Death: Right when you start up the game, a bloody red static screen is shown, displaying "The War Against Giygas!" As soon as you defeat Giygas, the same effect is displayed, ending the battle.
Spinning out of Here: Like in MOTHER, teleporting requires rapid, uninterrupted acceleration before zooming off to the destination, so areas with limited space to build speed require moving in circles to avoid crashing. One teleport ability requires the player to turn manually, the other one automatically makes the party move in a tight spiral.
Squishy Wizard: Again, Paula. Her PSI Freeze spells rip enemies into shreds, but her HP is so low that even two hits of PSI Thunder obliterate her. Hell, often her HP during the endgame can be maxed out by Lifeup-beta.
Standard Status Effects: As well as many non-standard ones. Characters can be affected by sickness, heat stroke, ghostly possession, homesickness (in Ness' case — this happens at random, and it's cured by calling Mom), mushroom growth, the common cold, uncontrollable crying...