Bag of Spilling: Inverted. In the opening cutscene, Grunkel is flying with a witch's hat full of keys to her house, but she drops them all and her magic wand on the way to her house. The Player ends up picking them all up.
Fantasy Kitchen Sink: Haunted Island is a grab bag of anything conceivably Halloweenish. Ghosts, vampires, and witches are to be expected, but an Egyptian pyramid? In the middle of a spooky forest with gnarled trees? God knows how that got there.
Fetch Quest: The game is mostly a series of these. You have thirteen classmates to save and four items are required to save one. You have to play three mini-games to get just one item. So in all, you have to play 156 mini-games to save all your classmates. On top of this, you have to play three rounds of all the mini-games, except for the pirate activity, to count as having played it once. So unless you get the pirate activity, you have to play nine rounds (three rounds for three mini-games) to get one item. Also, the game keeps track of which mini-games you're bad at and assigns those ones to you repeatedly. Yeah, it's a long game.
Guide Dang It: Early releases of the game only include the island map in the user's guide. Thus, if you don't have the user's guide, you can't navigate the island effectively and are pretty much screwed. (Clever form of Copy Protection, though.) Later releases dropped the user's guide and included the map in-game.
Healing Spring: The Fountain of Health in the Labyrinth, if you can find it.
Hollywood Darkness: Nearly everything on Haunted Island appears black and blue. That is, until you get close to it, which somehow makes it show up in full color.
I Resemble That Remark: The bugs in the spider spelling challenge protest this when Flap expresses doubt in Pomreeda's belief that the letter bugs are cute.
Medium Blending: The game constantly flips between CGI animation and 2-D animation. For the most part, the main game is pre-rendered CGI while the mini games are 2-D. The main characters (Flap, Ms. Grunkle, etc.) are always CGI. Your classmates look CGI in the opening sequence, but they are 2-D animated in the yearbook and Madame Pomreeda's Crystal Ball.
Laura becomes a vampire, except with two heads, one of them is her normal head and the other is a purple-skinned vampire head. When she transforms back to normal, her normal head turns around and EATS the vampire head.
Pirate Tropes: The geography activity is pirate-themed, so it includes a number of these:
Boarding Party: Implied. If you lose one of the cannon battle mini-mini games mentioned below, your ammo and supply counts go down.
Pirate: Type 1. The pirates are your enemies, and if you run into one of their ships, you'll have to sink it in a cannon battle mini-mini game.
Ghost Pirate: Possibly. You don't actually see the pirates themselves, but their ships are all white and ghostly. Oddly, your ship is too.
Pirate Booty: You have to identity the countries with this, based on the geography clues.
Pirate Parrot: Picking up supplies is accompanied by a parrot sound effect.
Talk Like a Pirate: Naturally. While you don't see the pirates, a pirate voiceover gloats at you during the cannon battle mini-mini game and follows this trope.
Oddly averted on your ship, where the only pirate you hear (presumably your first mate) speaks with a British Accent.
Treasure Map: The game is played on a parchment-looking world map, which nevertheless has modern-day (i.e. 1990s) countries and borders.
Retro Universe: Some of the children are explicitly from the modern day while others seem to be Disco Dans and they all go to school together in an old-fashioned one-room schoolhouse. The pirate activity seems to take place during The Cavalier Years, but none of the rest of the game does. Most of the stories you create in the cemetery activity are set in the present day. And, of course, the history activity has information updated to The Nineties (the time when the game was made) even though Flap says it was "a long time ago" that anyone was in there.
Status Cell Phone: One of Laura's items is a (now outdated looking) cell phone, which the game considers reflective of her Class Representative personality. When the game was made in the mid-1990s, prepubescent children owning cell phones was very rare indeed.
A blink-and-you'll-miss it mistake in this sequence: the boy named Joe turns into a silhouette that doesn't match his monster form. He's supposed to become a giant angry gorilla, but transforms into Stanley's form, a Frankenstein's monster instead.
Themed Cursor: As you can see from the screenshot, the game makes the cursor look spooky and ghostly.
Updated Re-release: Two years after its initial release, the game was rereleased with an onscreen leveling feature (previously leveling was activated by pressing "Ctrl-L") and an in-game map (previously the island map was only included in the user's guide)