Emmet seeing that none of his coworkers really like him or even know anything about him, and most of them don't even recognize him when asked by the police who he is. This hits even harder when Vitruvius reveals that he made up the prophecy, and Emmet is just like everyone else. Even the surfer guy he spoke directly to mere hours ago doesn't even know his name.
Gail: Wait, who is that guy? Does he work with us? I am so confused...
Emmet: Gail doesn't remember me?
Surfer Dave: I know that guy, but I know, like, zippy-zap about him.
While everything about Unikitty's relentless optimism is normally played for laughs, seeing her desperately trying to keep herself happy after her home is destroyed is genuinely sad.
The escape from the police as the gang leaves Cloud Cuckooland. They build a submarine within a minute, and Emmet can't contribute because no one offers him room to be heard. He tries to get a word in, but he's never used his creative side at all and no one's stopping to help him or listen to him until Vitruvius gives him words of wisdom! Not to mention it was Emmet who thought of going underwater first, and Batman steals the idea a second later, taking all the credit. You gotta feel so bad for him.
While not much attention is drawn to it. During the attack on Cloud Cuckooland, a unicorn can be seen running by the screen with it's back on fire. You can tell it must be real fire too because the poor thing whinnys in pain!
Later, when the submarine is underwater, Uni-Kitty sees what's left of Cloud Cuckooland. She's utterly heartbroken.
Unikitty: (ears folded, eyes teary) My home... It's gone! I feel something inside. It's like...the opposite of happiness! I must...stay...positive. (breathes) Bubblegums! (breathes) Butterflies? (breathes) Cotton candy?!
Emmet also watches the remains of Cloud Cuckooland and it's evident that he feels awful considering that he was the one who got a tracking device latched to him. He even tries to comfort Uni-Kitty.
The musicnote Titled "Requiem for Cloud Cuckooland", no less does not help either.
And then when Emmet reveals he built a double-decker couch, because that's all he knew how to do, and he looks so ashamed that he couldn't contribute in a meaningful way, and everyone gives him hell for it. ... yeah it's also funny, but only because literally everyone hates it.
The notion that Cloud Cuckooland's destruction may represent Finn's resentment toward cleaning up his playtime LEGOs.
Even worse, it could represent Finn's resentment towards moving. Where are his LEGO bricks? They're in a box labelled "Cloud Moving". He could have moved there recently.
It's barely noticeable but, Batman takes a moment to look at Uni-Kitty sadly as she starts to break down. While it's hard to see, you can tell his sympathizes with her as much as all the others.
And before that, Good Cop has his face forcibly removed with nail polish remover. The movie even focuses on the shot of the Q-Tip dissolving/smearing it away. Following this, Bad Cop cruelly glues his parents together.
It's easy to miss, but before Lord Business removes Good Cop's face, Bad Cop tries to switch in to protest, and the robots holding him down have to use force to switch Good Cop back in, and hold his head to prevent Bad Cop from coming back.
Although the Q-Tip did a terrible job of wiping the face off, it's still incredibly painful to watch Bad Cop struggle to get up from the floor while his parents watch in a mix of horror and grief for their son.
Shortly after being caught, Vitruvius is suddenly killed when decapitated by a penny thrown by Lord Business. What makes this scene shocking is how it abruptly follows Vitruvius's own personal Crowning Moment of Awesome when he takes out dozens of mecha-mooks. To make matters worse, Vitruvius was one of the few who supported Emmet and even tried to offer some parting words of advice before dying. Everyone becomes so disheartened that they didn't even resist Lord Business's mooks.
As he's dying, Vitruvius explains he made up the prophecy of the "Special", you can see Lucy, Benny, Batman and even Bad Cop all gasp in shock.
Bad Cop is the only one who's seen the footage of what Emmet's 'friends' thought of him. At the time, he thought it was the perfect cover for 'The Special'. Now, he knows that Emmet had no idea at all about anything he was interrogating him about.
This is mitigated somewhat by the fact that Vitruvius comes back as a ghost. Still, it's hard not to feel initially shocked and saddened that an experienced, likable character was killed off.
As Lord Business and his army attack Emmet's hometown, one of the people can be heard crying out:
"Please, please! Wont somebody help us?"
When Finn's dad goes over to the set his son has constructed and pulls off the Lord Business minifig, which is based on him, and sadly asks Finn, "So...Lord Business is the bad guy?", and Finn just looks away. He realizes for the first time just exactly how his son views him. And he's heartbroken. At the same moment, Emmet's speech—so Heartwarming.
When his dad looks back at him after tearing his son's creations apart, Finn is simply standing and doing nothing to the naked eye, but you can tell he's holding back tears... then Dad walks toward him, kneels down... and gives him a soft apology hug. Lord Business does the same to Emmet.
Emmet plunging into the abyss in order to save virtually EVERY MASTER BUILDER President/Lord Business and Bad Cop have ever captured and put into the Think Tank. For the next 15 minutes or so, all the other characters think Emmet's really dead!
Wyldstyle's heartbroken look when Emmet is about to throw himself into the abyss. She's spent most of the movie saving him at her chagrin because he's not the Special. And the one time she wants to save him, she can't. All she can do is beg him not to go, even if it meant that she would die.
The horrified, "please don't go" look on Wyldstyle's face right before Emmet leaps into the abyss.
"Wh-What do we do now? There's gotta be a bright side here somewhere."
After the Master Builders are saved, everyone is in shock as Superman helplessly asks if anyone has any ideas on what to do now. You know that if it's Superman saying that, they're in deep trouble!
"Emmet had ideas..."
Emmet's helplessness once he enters the real world. He tries to move or say something, but can't.
Finn's father ripping his son's creations apart. It's shown offscreen, and only in the Lego world as being swarmed by Micromanagers, and for good reason.
As this happens, Emmet is mentally begging Finn's father to stop it, because he's hurting his friends. He's completely motionless, he has to watch this, and there is nothing he can do about it. He sounds on the verge of tears. And Finn probably is too.
Emmet: Stop it! Stop it! Stop it! Oh, those are my friends! No, stop it!
Metalbeard (with the gang surrounded by Micromanagers): Ye were a hearty crew, but it... it be over.
The mere prospect of the Think Tanks. Imagine going from a crazy-creative, free spirit to a person whose life is spent having all their ideas taken from them and are completely unable to do anything about it. Congrats, you now have a clear picture of what the lives of many Master Builders were like.
The scene when the remaining Master Builders are taken to the Think Tanks. Try not to sob as you witness their half Oh, Crap!, half Tear Jerker faces.
Wonder Woman: Oh no...
The thing Finn's dad says to his son before ripping his wonderful creations apart. It's the way he says it that makes it so menacing.
The Man Upstairs: Finn, we're gonna play a little game. It's called, "Let's put everything back the way you found it."
When The Man Upstairs asks his son what a lowly construction worker is doing in the middle of the city, Finn protests—on the verge of tears—that Emmet isn't just a construction worker ("He's the hero!"). The Man Upstairs refuses to believe it, and tells his son point-blank that Emmet is just an ordinary construction worker, and that he wasn't meant to be anything better. When he just dismissively looks down at Emmet (who's seen as an immobile LEGO figure at this point), you half-expect a tear to roll down Emmet's cheek.
The shot of Finn's dad coming down the stairs. One half expects him to be an Abusive Parent
The In Memoriam at the very end for Kathleen Fleming, who never got to see the release of the film to rave reviews. Worse, she was only 39.