One of the Boos says the word Boo...in binary code.
Also, his name: ComBooter.
In the first Gloomy Manor mission, Luigi surprises a Greenie in the shower. After the two simultaneously freak out, the Greenie makes a run for it...and promptly smacks right into the wall that it was trying to phase through.
Gadd's motivational speech to Luigi. "With my brains and your...uh...your...hmm, we may be in a bit of a pickle..."
"...you have a really bushy moustache!"
In the Haunted Towers' first mission, there's a hole, where if you peek through it, you'll see a Slammer ghost banging wildly on a pipe organ. A Hider later takes up residence in said organ during the second mission, and occasionally pops out of the pipes as the Slammer keeps playing it!
In a later mission (B-3 Graveyard Shift), the window of the Gardener's Room shows a bunch of Greenies "rising from the grave" as zombies. The sounds they make are really silly.
Really, a lot of the shenanigans the ghosts are up to.
The Greenies, oh boy, the Greenies. They're always doing something cute, funny, or both!
In Gloomy Manor's studio, there are two Hiders, one painting and one modeling. The model annoys the artist by changing pose and peeking at the portrait. By the time Luigi gets to the studio, it's revealed that the artist Hider painted a spiteful mustache on his model's portrait.
There's a pendulum at the Old Clockworks. Launching the distressed Toad at the pendulum produces a gong sound and rewards you with a shower of bills.
At the Secret Mine, there is a hockey goal. Launch a nearby puck into it, and two Gold Greenie goalies will come out to play.
When Luigi discovers the teleporter system underneath the Secret Mine, he tests it by sticking his arm through it, seeing it come out the other portal...and then begins waving to himself back and forth and saying hi.
Professor E. Gadd has some good snark if you try to go the wrong way before a boss mission. "Sometimes, I wonder about you, Luigi..."
"Why the long face, Luigi? Well, genetics I suppose..."
Similar to the Greenie in the shower, Luigi will find a Slammer on the toilet in Treacherous Mansion's second mission. Said Slammer is also reading a newspaper.
And the method you have to use to battle the Slammer? Why, flush the toilet, of course. (Though it sends a spout of water out to hurt him, not sucking him in.)
When Gadd first plays Mr. Exposition in explaining where the fragments of the Dark Moon are, Luigi is clearly doing the "He's crazy" gesture behind his back.
King Boo decides to use a 3rd-grade bully insult before his fight.
King Boo: Why, if it isn't my old pal Luigi! Or is it Baby Luigi? I can't tell the difference.
After the first boss, the un-possessed spider queen leaves through a crack in the basement wall with some spiders. Luigi looks down the hall and sees a flood of spiders rushing to the crack and Luigi stands in the middle them frozen panicking the whole time. After they're all gone and he talks to Gadd, Luigi starts doing a goofy victory dance, when another spider drops in behind him. Luigi looks at it, screams, falls, and the spider just... walks off.
At the end, when the Dark Moon is restored, all the ghosts are shown changing back to normal. Among the ghosts shown is a Slammer chewing on a Greenie's head. When it realises what it was doing after changing back, he spits it out before giving it a hug.
Also, right before that, a Greenie in an outdoor area of the Secret Mine turns back to normal... and then starts shivering from the cold.
While the doll whose head follows you around the room in the Haunted Towers is creepy, you can make it unscrew its own head by circling around it counterclockwise.
Doing this gets you a gem. Helpful if you're going for 100%.
Luigi finds one of Gadd's Toad assistants trapped in the Clockworks factory. Said Toad is absolutely terrified of clocks, and is delighted when Luigi shows up because he thought he'd been forgotten.
Treacherous Mansion makes this even worse. Gadd instructs you to find the Toad assistant working there, who upon being rescued tells you that two assistants work there. And after you rescue both, Gadd thinks one of them is a ghostly impostor...
And even after he apologizes for that and says he's glad they're safe, he adds, "...I suppose this means I'll have to give them their paychecks now.."
In the final battle with King Boo, in certain stages, he'll slam himself into the ground to have steel spiked balls fall from the air. As much as the fight is awesome (and slightly terrifying), it's funny as hell to see one of the balls fall on him head-on If you're staring at him just as there's a shadow growing larger, right over him.
Just before sending Luigi into the Gloomy Mansion for the first time, Gadd tells Luigi to stop looking so scared because it's "just a few harmless ghosts." Then, Gadd thinks about what he just said and admits that it's actually several hundred dangerous ghosts.
At the end of the Secret Mine's third mission (D-3), Luigi becomes snowed-in and E. Gadd has to teleport him out. Gadd, realizing that Luigi must be frozen, offers to give him some time to warm himself up before his battle with the Shrewd Possessor. A few dialogue boxes consisting entirely of "..." is all the time Gadd is willing to give Luigi.
In general, E. Gadd's conversations with Luigi tend to be quite humorous, especially thanks to Gadd's absent-mindedness and Luigi's priceless reactions.
Any scene with the Polterpup.
Luigi: No no no, bad doggie!
The intro cutscene to the Overset Possessor fight. Luigi flies upward to the boss platform and flies through one of the panels sending the bird on it flying. The Possessor is behind that panel with a mischievous grin.
One of the Boos is named "Paraboola". In the American version, when he comes out, he says...
Paraboola: "I'm Paraboola! A symmetrical open-plane curve formed by the intersection of a cone with a plane parallel to its side! I mean... BOO!"
The animation when Luigi manages to capture a Boo. It doesn't quite fit, and he ends up using the Poltergust's nozzle as a pogo stick to force the Boo in, with the poor spirit making squeaking noises the whole time.
In one of the missions in Treacherous Mansion, Luigi can peek inside a hole near the balcony to find two Boos using the unfinished portal as a skateboarding ramp.
E. Gadd apparently doesn't know that Luigi really is a plumber, as right after B-1, he tells Luigi that he'd have a promising future as a plumber if "ghost busting" doesn't work out for him.
Booreaucrat, the Boo from E-3, is pretty amusing.
Booreaucrat: "Ahem...I am Booreaucrat! This mansion is now under the ownership of King Boo, esquire. I take it you have the proper credentials to be here, including ID and a mansion roaming licence? No? That's...unfortunate. You will have to be penalised!"
A cutscene of Luigi being pixelated in front of the Old Clockworks that you can get by chance has him being pixelated without his hat. He starts freaking out looking for it, then the hat simply pixelates on top of his head.