Chrono Cross/Fridge

Fridge Brilliance

 * The revelation that the  might actually address some of the game's conspicuous cases of Unexplained Accent.
 * The popular courting gift in Arni seems like a weird thing to have changed between worlds, until you realize that with Serge dead the only ones chasing after silly dating fads were little kids so it makes sense that they'd come up with something that doesn't involve fighting monsters.
 * It's actually pretty bugging when you go to the final boss, and see there's no music. This game was made by Squaresoft, y'know. A company known for making games with Crowning Music of Awesome, especially the final boss themes. But the Fridge Brilliance kicked in from an extremely trivial detail: it's from the way to defeat him. There's a little sound heard everytime you cast an Element - the sound differs in pitch for each color. If you happen to cast the Elements in the right color sequence, the sounds make the melody for Radical Dreamers ~Unstolen Jewel~. So there IS a final boss theme - it just doesn't play directly. - The Dead Skin
 * At first I was rather pissed off that the main story of Chrono Cross kills off Lucca and Robo. Then I remembered that they were killed by the actions of FATE, who was after the Frozen Flame. By getting the Golden Ending and performing a Ret Gone on the Time Devourer, you've essentially made the Frozen Flame powerless from the very beginning, meaning that, in the newly repaired timeline, Lucca and Robo are alive. - Zennistrad
 * The "Kid takes over the world" alternate ending seems silly until you realize that the only way to access it is in a New Game Plus, where all the playable characters have superpowered stats from the last playthrough. Given that, it makes sense that she'd be able to ; Lynx at that point is still a relatively weak midboss, and Kid would be strong enough to shrug off poison.

Fridge Horror

 * Some players on subsequent playthroughs never visit Water Dragon Isle until it is time to get the Blue Relic. There they find no dwarfs or fairies, just Lagoonites. After thinking about it the player realizes that the dwarfs killed all the fairies, then the Water Dragon killed the dwarfs in rage, using Lagoonites to do the deed.
 * Sky Dragon isle after visiting its alternate world counterpart, . Those statues were there the whole time...
 * The FATE Terminals (or whatever the save points were called) are stated late in the game as to manipulate people's brain chemicals and therefore influence their actions. Guess who's been using them more than anybody else.