This gem from the first encounter Valjean as Monsieur Madeleine has with Javert after he broke his parole and made a new life for himself as the Mayor:
Javert: It seems to me, we may have met...
Valjean: Your face is not a face I would forget.
The shit-eating grin on his face as Valjean/Monsieur Madeleine is saying that, and the "Haha...wait, what?" look on Javert's face as he receives the back-handed compliment.
Also, the emphases he puts on the last word of that line, "Forget" might be a callback to "Look Down", where Javert warns Jean Valjean to "NOT FORGET MY NAAAAME", which makes the line even funnier.
In "Master of the House", an unnamed guy playing Father Christmas in the street - replete with presents, wagon-sleigh and reindeer, etc. - gets lured into the inn by a prostitute and he is shown a good time. After the number, an epic Brick Joke happens: we see the very drunk Father Christmas again—now missing his hat, beard, pants, presents and wheels and down to only one reindeer—being dragged along on the wheel-less sleigh by said lone reindeer while drunkenly singing the chorus. He seems pretty happy, all things considered.
During the song, at "Residents are more than welcome / bridal suite is occupied / reasonable charges plus a little extra on the side," Monsieur Thenardier is seen hiding under a bed while the Santa guy has sex with a prostitute, robbing them. While this goes on, the prostitute gives a delighted cry of "Ohhhh, Santa!"
Compounding "Ohhh, Santa!"'s humor even further is the fact that this was put on the official soundtrack as well. A hilarious addition to a song that was already celebrated for its raunchy humor.
Later, when Valjean enters the inn, you can see the guy's false beard nailed to a post in the background.
When Mme. Thenardier says her husband "thinks he's quite a lover, but there's not much there," everyone steals a quick glance at Thenardier's crotch.
The entire "Waltz of Treachery". Highlights include Valjean quite calmly taking back the hat Thenardier tried to nick off him, and Cosette's indignant "I don't believe this" look through the entire thing.
Especially funny is before "Waltz of Treachery," when Valjean is saying that he's come to take Cosette away from the Thenardiers with Fantine's blessing, Thenardier is trying to get Cosette to come over to him and Madame, but she won't and when he tries this again and again, she shakes her head. She does it again when they're trying to convince Valjean she's sickly to get more money out of him, like "No, I'm not!"
There's this brilliant moment when Madame Thenardier drops her handkerchief, so Valjean will pick it up for and she'll pick his pockets while he's distracted. Instead, Valjean just gives her this Really? look, causing her to shrug sheepishly.
Upon being told by the Thenardiers that he's just missed Valjean after this scene, Javert visibly rolls his eyes.
Running Gag: Monsieur Thenardier's crippling inability to remember Cosette's name, instead calling her "Colette". Madame Thenardier has to correct him at least three times.
Most amusingly, "Farewell, Courgette!" Which is a Bilingual Bonus: "Courgette" means zucchini.
Not really a bilingual bonus, since most of the characters speak British English, which uses 'courgette' rather than 'zucchini'.
During "Javert's Intervention", Javert randomly picks up Gavroche in the middle of his lines. The utter look of disbelief on Gavroche sells it!
During "The Robbery", there's Javert's "You Have Got to Be Kidding Me!" expression when Thenardier says "In the absence of a victim, dear Inspector, may I go?" and tries to clean his jacket - and his face - with spit and a handkerchief. It's like he can't believe this homeless creep actually just did that.
And before that, when Thenardier says, "The child what was stolen from me," Madame Thenardier says, "Yeah, and me."
Enjolras' exasperated expressions as Marius sings during "Red and Black".
And Grantaire's shit-eating smile and ridiculous expressions as he goads Marius, staring right at Enjolras as he does.
Eponine's puzzled look when she enters just as the song ends.
When Enjorlas sings, "Don't let the wine go to your brains", he looks pointedly at Grantaire.
Marius adorkably stumbling over himself during his first face-to-face meeting with Cosette in "A Heart Full Of Love".
An Out-of-Character Moment when Cosette raises her eyebrows when Marius tells her "I don't know what to say". The supposed to be pure, innocent Cosette clearly knows she has this effect on guys.
Marius grabs the red flag during "One Day More". The woman darning it wasn't amused.
Grantaire is not present during the funeral procession scene. Where is he? Back at the Cafe Musain with a waitress sitting on his lap, to be rudely interrupted when the others come rushing back with soldiers on their tail.
When Valjean spots the Army snipers and the students begin trying to defend themselves, this little gem can be heard amidst the chaos.
Marius:To your right! No, Grantaire, your other right!
When Valjean and Marius fall into the sewers unconscious, Thenardier is already there to go through the presumably dead men's pockets. Then Valjean comes to...
Thenardier: Oh, you're alive? I saved you!
The way "Beggars at the Feast" is choreographed. Instead of the Thenardiers leading the guests in a raunchy dance like the stage version, Marius has his servants carry them downstairs and throw them outside. The entire time, they continue to sing about how they're totally the ones who always succeed.
Thenardier: How dare you!?
The dying Valjean booping Cosette's nose.
The fact that this heartrending musical based on a ridiculously tragic book was released on Christmas must have felt like a cruel joke for first time viewers.
When Javert kills himself, as he hits the water there's a sickening CRACK! sound...it's a powerful scene, until you watch it again. IT'S THE STOCK BONE CRUNCH SOUND EFFECT, just pitched down slightly while a bit muffled.