The Cameo: Athena and Kensou (fresh off their debuts in Psycho Soldier) appear as two of the four Sages. However, Athena is called "Asina" and Kensou is rendered as "Kensu", a clear case of Engrish.
The village elders of two towns are also named Ralph (Ralf) and Clark, the Ikari Warriors-originated soldiers who're now far better known from King of Fighters.
Charged Attack: Every sword comes with a base level 1 charge. Most can charge to a level 2 attack after you acquire an orb to go with said sword (except the Crystalis sword, which also automatically comes with this), and the four elemental swords can hit a level 3 charge when an appropriate bracelet is equipped.
The Crystalis sword's apparent three charge levels is the result of a glitch and the sword was always meant to have just one charge level. If you go into your inventory (or the status screen) and come back out, the "extra" levels of charge disappear. Furthermore, assuming you have a bracelet equipped, if you avoid going into your inventory between receiving Crystalis and the battle with DYNA, you'll find that the "extra" levels do nothing.
Cowboy Bebop at His Computer: The manual! The story given in the manual is completely inaccurate and, in fact, makes the story in the game harder to understand! (Why would Draygon be searching for the tower if he built it?)
Four Is Death, on both sides: There are four benevolent Sages, but there are also four evil generals who work for Emperor Draygon.
Forced Level Grinding: In the NES version, you cannot damage enemies or bosses if you aren't sufficient level. The GBC version averts this.
Giant Space Flea from Nowhere: Emperor Draygon is definitely the Big Bad, and has been for the entire game... until right at the end, when you kill him and then get whisked off to the flying tower. The actual final boss is the tower's computer, DYNA, who also happens to be ridiculously easy compared to Draygon.
Heroic Mime: Mostly played straight, as the hero has all of four lines, three of which are used to tell mortally wounded characters (first an Almost Dead Guy on Mt. Sabre, later Stom and Akahana in Shyron) to STFU if they want to maximize their remaining time before having a Critical Existence Failure.
Hero of Another Story: Kensu, right up until the point he teaches you Flight. Whereas the other wisemen dedicate themselves to helping the hero, Kensu takes on the Empire himself. If not for a lucky shot from Karmine, he might have freed the other wisemen himself after Shyron fell.
Humans Are Ugly: The elder of Oak doesn't like the smell of humans. In the GBC remake, it's one of the residents blocks the elder's house claiming he doesn't like that smell. That resident doesn't like the smell even after he accepts that humans are actually nice.
Improbable Power Discrepancy: Averted. DYNA is a pushover, and its only defense is a set of gatling guns. You easily defeat it with Crystalis, which the game manual notes is the most powerful weapon ever created.
King in the Mountain: Your character — and Mesia! — are asleep until the time comes to either save the world or destroy it.
Lady Land: Amazones. They insist that men are forbidden in town, but you're still free to purchase goods or rest at the inn.
Mana Potion: Fruit of Power restores part of your magic. Magic rings restore all of it.
Magical Mystery Doors: GBA port, in the floating tower. While each floor and door does look different, the correct path is marked by broken pillars with exposed wires. The final floor is a set of three doors with no indication which one is correct.
Magic Versus Science: The skills in the game include an array of common psychic tropes but are referred to in-game as spells, seemingly an innability to decide which they are if either. This could mean that these abilities are thought of as both or it could be a Shout-Out to Psycho Soldier due to the cameos made by Athena and Kensu.
Mind Screw: "Wait, were Azteca and Draygon the same person, or were there minds linked somehow? And how does that work if Azteca was really a robot the whole time? And why was he a robot any damned way?! I'm so confused!"
La Résistance: Hero, Mesia, Zebu, Tornel, Asina, Kensu, Stom, and possibly Akahana. Whether Azteca was truly a member of the resistance is unclear due to his connection with Draygon, who also may have been his elaborate alter-ego.
No Ontological Inertia: The GBA port has General Kelbesque cast a spell on Zebu that disintegrates him into a million pieces. Defeating the general causes Zebu to be restored (and appear in the next room.)
Tomato Surprise: In the Tower it is revealed that the Hero was one of the scientists who built the thing in the first place. Your job after awakening was to judge whether the remnants of humanity were worth saving and if the answer was no, to use the Tower to wipe them out. Being the Hero, you destroy the Tower instead.
Two Aliases, One Character: Portoa's Queen and the Fortune Teller both appear, but not at the same time and keep referring you to the other alias. Eventually, the dialog will start looping, requiring the hero to double back and use the newly acquired paralysis skill.
Upgrade Artifact: There are magical orbs and bracelets that can enhance the magic of your swords, and will be required to access other areas in the game.
Villain Exit Stage Left: The Draygonian bosses, unlike the other boss enemies you face, flee upon being defeated the first time except the last one, who's only fought in Draygon Castle. You only get to take them down for good the second time you face them.
Welcome to Corneria: Using telepathy in the GBA version always gives the same message all the time. This was not the case in the NES version, where the advice changes as you progress through the game, and where one of the contacts could remotely restore your MP.
What Could Have Been: Back when SNK thought the Neo Geo might make it as a console (and not just be used as a cheap arcade machine) there were plans to remake Crystalis for that platform.