When Leo first cornered the party with his Dragonship Destiny, and ready to fire to obliterate them. Suddenly lightning bolts struck from above and disabled the ship's weapons. Leo's men were scared, but Leo assured them that they were Althena's chosen, and no harm would come to them. Cue multiple lightning bolts zapping Leo to unconsciousness. Turns out a Villainous Rescue by Ghaleon.
"Listen up, soldiers. Our fugitive has been on the run for a short while. She's in here somewhere. I want a low-level search of every bird house, dog house, outhouse, tree hourse, hen house, road house, boat house, and penthouse within a two-mile radius! We shall capture this rogue and her cohorts!" It might be another reference, but this one withstands the test of time way better, even if you don't know what it's referencing.
When the party goes to Taben's Peak to find Nall, they are ambushed by some kids. The kids' weapon of choice? Pinecones, naturally.
Kid Leader: Defense squad! Concentrate your attacks on the dumb-looking guy!
*Ronfar falls off the ladder after being repeatedly hit*
Kid Leader: HOORAY! Defense squad, retreat!
Ronfar: That...REALLY hurt...but I still have sensation in all of my most important extremities.
A book in the library of Lemina's magic guild lecturing on the importance of resource conservation is titled (or sub-titled) "Don't Toss That Pad!"
There's plenty of other hilarious books there too. One of the better ones involves a man making a claim about green bug-eyed aliens from the Blue Star abducting and Anal Probing him, eliciting a bewildered "What?!" from the normally stoicLucia.
Zophar: Psst. You. Yes, you. I see what you're doing. Ripping XA Audio from the CD, illegally listening to it without legitimately finishing the game. You wanted to hear those outtakes so bad, you couldn't wait. I like that. Cheating is good. You know when you cheated on that test in school and thought nobody was looking? I saw it and I remember. When you lied to your parents and you thought you got away with it - you didn't. But I liked it. And now you're cheating with XA Audio. Where does it stop?! It doesn't! That's the best part! I have a place just for you. A nice warm place right at my side. Hahahaha. MWAHAHAHA!