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.
Nice Job Fixing It, Villain: Giygas abducts Dr. Andonuts, Apple Kid and one of the Mr. Saturns and places them all in Stonehedge. This allows the three of them to meet and develop the Phase Distorter, the device that sends you back in time to defeat Giygas.
"are totally scrapped" or "are destroyed" (war machines)
"go back to normal" (angry/brainwashed people)
"return to the dust of the earth" (zombies, mummies, etc)
"melt into thin air" or "disappear" (gases/ghosts)
"are defeated" (everything else)
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.
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...
"Yes, you will. No, you will...not. Yesno, you will won't."
Playable Epilogue: After the final battle, you are free to roam the entire world as you please, with no enemies in your way, until you decide to visit Ness's mother. (Actually, if you ignore the Shattered Men in the Summers Museum, they'll still be fightable in the epilogue, which if you purposely die crashes the game. And may trigger other glitches.)
Police Are Useless: Not only do the police not seem to be able to handle things like kidnappings and teenage gangs, they actively get in your way by setting up pointless roadblocks.
Police Brutality: When Onett's police force is asked by a teenage 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.
Pronoun Trouble: Due to certain lines of battle text being used by more than one enemy, we sometimes get lines like this. Similarly, having Paula use the Ruler or Protractor will cause the game to refer to her as "he".
Psychic Powers: Instead of magic characters use Psi. Paula also uses telepathy at a couple points.
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...
Random Effect Spell: Pray, on the occasions when it's not used outside of the final battle. Mostly it either does nothing or heals everyone a little bit, but it can also cause status effects on your part, revive everyone (including enemies), recover all HP and PP to someone, and other things.
Psi Flash, when it hits, may inflict crying (blindness), numbness (paralysis), feeling strange (confusion), or unconsciousness.
Raygun Gothic: The style of the Starman and the robots seems to be based around this.
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.
Skyscraper City: Fourside. You have to find your way to the top of the biggest one in the city too.
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.
Spoiled Sweet: Paula. She is famous and her dad totally babies her, but she is very serious about saving the world no matter what it takes.
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...