Gokudera: I got ran over a few times on my way here!
Reborn: Wow Tsuna, you got some skills out there, getting yourself hurt in the hospital.
Ryohei: The dolphin has guts. I want him in my club!!!
Squalo giving Dino a tuna as a souvenir. Tsuna's reaction is the best "Why a tuna?"
The absolutely nonchalant way he hands it over ("It's a gift.") is what sells this scene. Then he goes and beats Yamamoto into unconsciousness, hauling his limp body off like a sack of potatoes for some training. The whole scene is only a few minutes long.
Gokudera: Anyway I don't like that guy.
Tsuna: Huh? Why not?
Gokudera: Anyone older than me is my enemy.
Tsuna: [shocked and thinking to himself] God! That's a lot of enemies!
Gokudera's nickname for Lambo being "Stupid cow".
The way his voice actor says "ahoshi!" (stupid cow).
Anytime Gokudera looks at his sister and gets a stomachache.
A funny Narm moment: After Tsuna epically punches Daemon several yards underground, the next panel is simply "YOU BASTARD!" coming from the hole created.
Chapter 366: Byakuran's attempt at searching for Mukuro involves blowing up a random car. Cue person running out of it while on fire.
Byakuran: Guess not, just an ordinary person~
Then there's the "Bowling" chapter, where Longchamp invites Tsuna and Gokudera to go on a three person blind date. Of course, Longchamp's idea of a "cute" girl has always been... unique. So the three girls he invited were absolutely hideous (one of them even being Reborn in an ugly drag). The whole chapter pretty much consists of Tsuna and all of his Bishōnen guardians / male friends coming by, being horrified by how ugly these women are, and then trying to run away from them as the women aggressively pursue them.
Technically, it is true that Reborn didn't see him.
Chapter 380: Everyone's reactions to Flan sleeping. Even Mukuro gets Blank White Eyes!
In an early chapter after Tsuna saves Gokudera's life Gokudera becomes devoted to Tsuna and says he'll place his life in his hands. Tsuna doesn't want this but Gokudera glares at him and Tsuna is shown thinking "Too...Too afraid to refuse...What kind of situation is this..."
Reborn's tendency to fall asleep whenever Tsuna is talking. In Chapter 391 after Tsuna makes his declaration that he won't let Reborn die Reborn responds by falling asleep complete with Snot Bubble.
Tsuna cannot tell who Adult!Reborn is. Chapter 402, and the Arcobaleno are doing their job to make sure it stays that way.
Hibari thinks the way to increase his flames to activate his ring is to get pissed off. Kusakabe and Genkishi immediately think together "That's wrong!!"
When protecting Yuni, Squalo and Hibari step up to protect her and Tsuna. Except Squalo is more in front and didn't notice Hibari. Hibari, instead of beating Squalo, pokes him with his tonfa and tells him to get out of his way. It's his vaguely polite expression and Squalo's reply to being poked that makes the scene funny:
Squalo: "Stop poking me!"
Fran's Image Song, Special Illusion, is basically a song about fucking with people for the fun of it, specifically mentioning Bel twice.
Speaking of image songs, Gokudera's song, "...loop" sounds like something he was goaded into singing at a karaoke bar by Ryohei and Yamamoto. If only because the pace and melodramatic way in which he sings is so out of step with Gokudera. He even expresses disbelief he sung at the end of the song.
When they first meet, Gokudera thinks Shitt. P! is really an UMA (that is, an Unidentified Mysterious Animal) and continues to think this from then on to Tsuna's surprise. Sometime later, Gokudera fights her and it's revealed after the battle she thinks he is an UMA (specifically, she thinks he's a "warm UMA"). Gokudera and Tsuna are both hilariously shocked by this.
There's something hilariously cute about Mammon wearing a little sun hat when going to go pick up Fran with the rest of the Varia. Note that Mammon is wearing it and the hood of the robe. Thereby implying someone (likely Bel) stuck the hat on for some reason, and Mammon just didn't care to remove it.
Every reminder that Yamamoto thinks the mafia is really a game.