- Nadia using her last ounce of strength to push Roshan over to Manny in hopes that he will be saved,
- The Art Shift Flashback in the cave that reveals Manny's Dark and Troubled Past. Even Diego has tears in his eyes at that scene.
- Diego taking the mortal blow for Manny during the battle with Soto at the end to protect him, as it is obvious that Soto's incisors slashed him fatally, and let's not forget that blow to his head that he got. And as he dies (the commentary for the first film confirms that he actually did die in that scene) he selflessly insists that Manny and Sid forget about him, since he wants to make sure Roshan gets home as much as they do now. This scene is especially heartbreaking if you remember that Manny has only recently lost his family, and now he is losing someone close to him all over again. His brimming eyes as he watches Diego leave them only serve to drive the point home.
- Young Ellie's flashback; a lost Mammoth calf all alone in a blizzard.
- A Genius Bonus for wildlife buffs - Opossums give birth to many, many babies - and the reason they seem to have six at a time is that most infants don't reach a teat in time. For Ellie's possum mom to only have Crash and Eddie left when they met, means something tragic must have happened to her litter. From a maternal point of view it explains her taking in Ellie.
- This one may sound crazy, but the montage of the acorn "observing" Scrat and Scratte's moments together, accompanied by a rewritten version of Gilbert O'Sullivan's "Alone Again (Naturally). You can feel sorry for an acorn!
- Manny's realising how much of a jerk he was to Sid lately, therefore causing him to steal the eggs and get kidnapped by Momma dinosaur.
Manny: (to Ellie) I'm sorry. I wanted to keep you safe...and here you are in the most dangerous place in the worldEllie: Hey, this isn't your fault. It's bigger than both of us. We have to get Sid.Manny: Yeah, well, if I'd been a better friend to him...we wouldn't be here.
- Sid's family return... to dump Granny with him, and get as far away as possible. Sid's reaction to being told this?
- Ah, they wouldn't do that! That's just mean, that's just cruel. That's just... my family.
- Peaches blaming herself for being separated by her father by the earthquake after a harsh argument with him that resulted in her disowning him. Even Ellie is trying very hard to suppress her own sadness and worry as she tries to calm her daughter.
Peaches (sobbing): Mom, this is all my fault! If I had just—
Ellie: Peaches, this is NOT your fault. Okay?
Peaches: What if I never see him again? And the last thing we did was fight!
Ellie: Hey, your father is the toughest, most stubborn mammoth I've ever met! He'll come back for us. That's a promise.
(Ellie wraps her trunk around her daughter with a look of sadness and worry of her own)
- As the group drifts in the sea, Sid asks Granny why their family hates them. Granny pauses, and in a moment of genuine clarity, admits she knows their family considers them nothing but screw-ups.
- When Manny with everyone returns to find the bridge where he told Ellie and Peaches to wait for him destroyed with no sign of either one of them; for a brief moment he closes his eyes, clearly thinking he's lost his family a second time. The others also look sad as well, even Granny, who just joined the group and shows further proof that she's not really as crazy as she seems.
- Peaches tries to impress the mammoths by denying her friendship with Louis; unfortunately, he hears her, and then leaves, looking utterly crushed.
Louis: (sadly) Good to know. (begins to tunnel away)
Peaches: Louis, wait!
- After Sid's Granny ends up on the crater nearby the meteor that caused the KT extinction event in the middle of the night, the Herd are unable to find her and when they lose track of her scent nearby the carter, Sid is heartbroken and begins to cry when they assume she fell to her death, thankfully she was alive and well.
- Sid saying goodbye to Brooke and to his granny who decided to leave the herd and stay with Shangri Llama and the others citizens of Geotopia.
- When all hope for save themselves from the incoming extinction event seems lost, Peaches begins to cry at the thought she will be unable to marry Julian and start living their life together.
- By the same token, Manny and Ellie gently agreeing that it's been a good life.