The scene where Kyle takes on monsters while wearing a ugly and unconvincing Wholesome Crossdresser disguise, trying to make his voice sound feminine and spouting stock damsel-in-distress phrases.
The scene where you first find the white dragon and ask for a diamond only for him to comment when you leave; 'Why humans are so interested in my leavings I'll never know."
The line is slightly different in different versions: "Why do you humans prize these things? Don't you know they're made from my..."
From Silver Star Story Complete:
Nall: "Nash... you suck."
The group's conversation upon entering Lyton and hearing the terrible music that's playing.
Nash: Do you think stuffing blades of grass in my ears will help to stop the bleeding?
Kyle: What are you guys talking about? This music's great! In fact, I'm gonna sing along! *belch*
Nall: Thanks, Kyle, now my ears AND my nose hurt.
Kyle drops this gem late in the game, when Xenobia captures Jessica and Mia and Kyle and Jessica distract her with their arguing long enough for the girls to escape.
Jessica: Wow, Kyle. I had no idea you were such a talented thespian!
Kyle: Thespian? Aren't I the wrong gender for that, Jess?
The original version has a scene where Mia asks Alex for help restoring her mother's sanity. It's a But Thou Must! moment because Nall won't let you leave your cell until you agree to help her. His comments telling you to help her already get downright hilarious. Some of the more notable excerpts:
Alex, you are a foolish, pig-headed, self-centered, small-minded, perverse, snot-nosed, egocentric brat! I hate you right now! Alex is a girlie man! 'Oh, no Mia, I cannot help you save your mother. The monsters in the spire are too strong! They could flick me across the room with just their pinkies! Then I would be left alone in the dark, crying in my baby poop.' .........................I'm hoarse.....You fool.....!!!! ...who are you? Has your body been snatched? I don't know this Alex... Someone I don't know is talking to me... who can it be? I don't want to hear anything but yes! Tap me when you want to say it. Lalalalalalalala.... Luna told me not to talk to strangers? Do I know you?
From the Sega CD release, a bookshelf in Damon's Spire:
Volume 15: Common Sense Video games will eventually rot the minds of all they enslave. At least that's what they're saying now...
Virtually everyone's attempts at making a sculpture of what they consider to be a "priceless treasure" to pass Damon's test.