- Upon first seeing Shingen practicing Kendo full-out against an opponent, and pretty much wiping the floor with the guy:
Logan: He's good.Yukio: He's alright.
- Logan discovers Noburo's debauchery and interrogates him about Mariko's attempted assassination.
Logan: You've got ten words to explain to me why you, the Minister of Justice, would want your fiance killed by the Yakuza. Now, if I don't like what you say, you're going through that window.Noburo: You don't have the faintest idea what's going on-(Logan punches him square in the face)Logan: How many words was that?Yukio: Nine.
Noburo: I told you the truth!Logan: I didn't like it.
- Once Noburo has spilled the beans, Wolverine pitches him off the balcony anyway.
Yukio: How'd you know there was a pool down there?Logan: I didn't.
- Then a splash is heard offscreen, along with a nod to Diamonds Are Forever's Plenty O'Toole.
- It's brief, but during the fight at the funeral, at one point Harada is covering Logan as he leaps into a room to take out the guys trying to get away with Mariko. Harada draws his bow and looks ready to fire a shot to help Logan...but after about ten seconds, Logan's carved up most of the guys and is already working on the rest, and Harada eases up on the bow without firing, the expression on his face clearly along the lines of, "Oh. Well, nevermind."
- After the Traintop Battle, Mariko and Logan end up in a love hotel. The only vacant rooms are "The Dungeon", "Nurse's Office" and "Mission to Mars." They awkwardly pick the last one.
- When they go in, Mariko approaches the rotating bed and Logan looks awkward when some recording says "Liftoff! We have a liftoff!"
- When Logan passes out from his injuries, the front desk lady brought her veterinary student grandson to patch him up. It's a Wolverine, after all! When Logan offers to shake the young vet's hand, the latter backs away in terror because Wolverine apparently unsheathed his claws and hurt him while unconscious mid-surgery.
- Logan's entire bath-and-shave hygiene session in the Yashida residence. He later quips, "I feel violated."
- There's some Bilingual Bonus as well that makes it even more hilarious. One of the ladies says: "It feels good, right?" ("Kimochii deshou?").
- Hugh Jackman's remarkable performance making it look a lot like trying to bathe a cat in general.
- Also when he gets scanned by the wands. He's never had a good relationship with metal detectors, so while the guards are freaking out, he just deadpans, "Hip replacement."
- Logan sticks the chopsticks upright into his food. After Mariko gently corrects him, he did it again!
- While on the bullet train, Logan tricks a Yakuza to jump to avoid being struck by a low-hanging sign, only for the unlucky bastard to get struck by a higher up sign.
- Logan enjoying the reclining train seat.
- Also in the traintop battle, the brief cut to Mariko in her headphones while a Yakuza roars at the glass in impotent rage.
- Another moment where a Yazuka punches Logan in the nose, there is a distinctive metal clang.
- "Go fuck yourself, pretty boy."
- Logan calling Noburo Nostromo.
- A Japanese man mistakes Viper for a prostitute. She gives him a passionate kiss... which literally kills him.
- The sad but funny fact that there's little Wolverine can do to stop Magneto from halting him when they meet yet again during The Stinger.
- In the stinger, Logan is in an airport security line. Taking one look at the metal detector, he tells the TSA agent, "I'll take the pat down."
- During Logan's self surgery, he remarks to Yukio, "You're not gonna want to watch this part", which is borderline Leaning on the Fourth Wall.
- During the Final Battle, Wolverine takes the Silver Samurai's spare adamantium sword, activates it and utters "Hey, bub!" before beheading the armor's helmet.
- When Logan is having a rant in the bar:
Logan: Go ahead, ask me were I found it. Ask me.Red Beard: Where did you find it?Logan: Well, funny you should ask.