"Brain Drain", because Brainiac 5 minus proper functioning is way funnier than it's really supposed to be.
Bouncing Boy screaming like a girl.
How about when Lex Luthor's great-great-great-granddaughter sticks her tongue out at Superman ("Sundown, Part 2"), because he dumped her.
In "Champions", Phantom Girl acting like a stereotypical hick to mock Superman when he pulls the Adorkable farmboy thing (after meeting her mother Winema Wazzo, the President of the United Planets) is much funnier than it should be; the look on her face sells it afterwards:
Phantom Girl: (acting like a Deep Souther sarcastically) "Aw shucks, ma'am. I ain't never met nobody! Uh-huh! Uh-huh!" (grins at Superman smugly)
It helps that during that bit, Phantom Girl is way more expressive than usual.
Lightning Lad's greatest fear? A little doll!
Considering it's a clowndoll named Captain Howdy, he may have had a very good reason to be afraid of that thing when he was little.
In "Unnatural Alliances":
Imperiex: "I believe you have have something I want."
Lightning Lad: "This energy cloud has brought us near the planet where my brother and I were infused with our powers ten years ago. ... It's also where we lost our sister, Ayla." Kell-El: "... You're not going to start crying, are you?" Lightning Lad: (continues talking as if he didn't hear him)
Also, when energy cloud!Ayla is begins singing the nursery rhyme:
Superman X: "THE CLOUD IS SINGING?!" Bouncing Boy: "Creepy."
Later, when Garth and Mekt join forces to restore Ayla, Bouncing Boy ribs on an unamused Superman. Kell-El's deadpan delivery is what nails it.
Bouncing Boy: "Aww, now that's not a tear I see from the tough guy, is it?"
Superman X: "Nope."
In "Timber Wolf":
Bouncing Boy: "Don't leave the hangar, huh? I can see why."
Brainiac 5: "I assume we'll be snooping?"
Bouncing Boy: "Oh yeah."
Timber Wolf and Star Boy messing around during one of the Legion meetings in "In Your Dreams."
Brainiac 5: "I'm sorry, am I boring you two?"
When Lightning Lad jumps ship to the Light Speed Vanguard in "Lightning Storm", Superman and Timber Wolf decide to tail him and spy on the group, who aren't doing much of anything at the moment.
Superman: "So what you do want to do while we're waiting? Play some checkers?" Timber Wolf: "What's checkers?" Superman: "It's a game we play in Kansas." Timber Wolf: "... What's Kansas?"
One of the auditioning recruits is Breath Boy, who boasts that he can hold his breath for long periods of times. When he starts demonstrating his ability, he is promptly dismissed. By the end of the episode, he's still there holding his breath!
The entirety of "The Substitutes", where the rejected Legionapplicants (the Legion of the Substitute Heroes: Porcupine Pete, Infectious Lass, Chlorophyll Kid, Stone Boy, and Color Kid) get A Day in the Limelight and deal with the whimsical, "third-rate nuisance" Starfinger whose furry minions unknowingly are the ionosphere-eating monsters the Legion has to deal with. In short, "Hilarity Ensues: The Episode."
Kell-El's increasingly terrible pronunciation of a simple counter-spell ("Magica Absistas") in "Trials."
Zyx: "Wow, that is shockingly bad."
"Chain of Command"
Bouncing Boy's reaction to winning the legion election
Bouncing Boy: I demand a recount!
When it turns out that Bouncing Boy being elected leader is no mistake, he repeatedly asks if it is true until the other Legionnaires yell at him that it is true in annoyance.