As he's fighting off an entire army of Warhoons, flashbacks show John finding his home destroyed and his wife and daughter dead. The subsequent cuts of him burying his family paired with Michael Giacchino's score (particularly the cue "Carter They Come, Carter They Fall," if anyone's curious) during this scene will guarantee you reaching for the tissue box.
The near-Downer Ending where a Thern uses the teleportation medallion to send John back to Earth after he threw away his own teleporter after deciding to stay on Mars with Dejah. There is also John's joy at returning to Mars in the end.
John's initial reaction upon his return to Earth is to let out a Big "NO!". His attempts at using the activation code without the Thern device leaves him in tears.
The scene where John accidentally kills a Thark, and he and Sola are branded. Sola already has brandings, and the next branding will kill her. She looks at John like she was contemplating if her keeping him was worth it. He's never seen apologizing on-screen, but the look of shame on his face when he's told what this all means is enough.
Colonel Powell, the Cavalry officer whose life John saved and in return warned him of his incoming attacker back on Earth? He died alone.