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Tear Jerker: Falling Skies
Rick's breakdown. After he's given up all the information he has to the harnessed girl, she leaves him in the dirt, utterly breaking his spirit: he only wanted to belong with someone. Now, the only people that he ever felt like he was a part of have no use for him, his father is dead, and most of the humans view him as a traitor.
Rick: [sobbing] "I... I miss my dad..."
Tom: "Hey, hey, its all right. It's all right now."
Jimmy's funeral in Season 2, Episode 3, including the eulogies from Weaver and the breakdown of Ben at the end of the episode.
When we find out that the skitters are also enslaved children, just of a different species, which makes the brutality of some of heir deaths even more tragic.
Red Eye's death during the season 2 finale is surprisingly heart-wrenching considering he's a Skitter.
Before that, the Skitter massacre. The fact that there's no way to find out who's responsible, the fact it almost ruined the assault on the Overlords, and the fact that, among the victims, were harnessed humans (showing that, whoever was responsible, Would Hurt a Child).
Just look at Col. Weaver's face when one of his fellow soldiers dies in his arms; To make things worse, Pope keeps throwing the blame of the Mech ambush on him. After the battle, even Pope realizes he should just keep his mouth shut about this.
The death of "Crazy" Lee.
Cochise is asked what he fights for. Cochise, the Spock Speak full alien who hasn't had much meaningful dialogue since he appeared, deliver us this:
President Hathaway: What are you fighting them for, resources, territories..?
Cochise: A flower, the "Catarius". It blooms on my homeland when the weather begins to warm.
Hathaway: A flower so valuable it caused a inter-galactic war?
Cochise: The Catarius has no value to anyone, except me.
Mason: Something you remember from your childhood?
Cochise: Actually, I have never seen it. Just as I have never held the soil of my homeland in my hands. Like the rest of my comrades, I was born in a ship that has left our world hundreds of years ago. All that I know of the Catarius is an image in a datafile...and a poem my brother read to me when I was young.
Mason: You never told me that you had a brother.
Cochise: He...he is deceased; on a planet orbiting one of those spots of light up there. A most weary, unbright cinder, far from the home I have never known. He was born to war, grew up in it, and it eventually claimed him. He died for a world he never saw. Be thankful that you fight on the soil of your homeland, gentleman. That is a gift. I will never see my home, but, if we win this war, my children of my children may one day, gaze upon the real Catarius. That is what I'm fighting for, Mr.President.
In "Strange Brew", Tom breaking down over the supposed death of Anne and Lexi and his visions of his long dead wife.