- "Out of Time", when John Ellis breaks down upon meeting his now aged and senile son, and Jack comforts John as he commits suicide and when Diane leaves.
- "Captain Jack Harkness": the saluting scene and shortly beforehand the kiss. The desperate look in Real!Jack's eyes. And the dance. Oh, the dance. The spotlight shining down on both of them, and everyone else stops dancing, just to watch. It was beautiful and heartbreaking at the same time, since we know what happens the next day. Unfortunately, it's quite possible that Real!Jack, having outed himself so spectacularly, was killed by his own troops.
- "Tell my family...I love them" written by Toshiko in her own blood in case she doesn't come back.
- "Remember me as I am. Remember Beth."
- "Cyberwoman". Watching Ianto's single-minded obsession with keeping Lisa alive, all in the vain hope that somewhere, beneath that cold, monstrous cyber programming is some shred of the woman he fell in love with... Dear God....
Lisa: Hold me, Ianto. I need you to hold me. I need you to tell me it's all right.
- And as justified as Jack was in killing Lisa, he knows that Ianto is equally justified for hating him for it.
- The "You're my brave, handsome hero" scene with Toshiko sitting on the bed in "To the Last Man".
- "Sleeper" is a very tear haunting episode as a whole.
- "Adrift" Gwen reunites a mother with her time-displaced son, who has (unbeknownst to Gwen) gone insane and the mother can't handle it and ends up rejecting him, even though he still loves her.
- A little clarification: a mother loses a little boy, and when she gets him back, he's a horribly disfigured middle-aged man. In spite of this, she still loves him and wants to take him home with her...until she learns that he's been driven mad by his experience in the rift, and screams for twenty hours every day.
- The boy's mother packing up his belongings at the end of the episode.
Gwen: I thought you wanted to know what happened to him.Nikki: I did. I was wrong. It was better when I didn't know. Before you, I had hope.
- "Adam" the final scene is tear inducing, as Jack opens up the mystery box at the end of the episode and finds it full of sand from the beach where he grew up. And because of the events of the episode, he has no idea what it is or its significance.
- When Jack passes out the memory pills to his team..
Tosh: Knowing there has to be more to life than this. Knowing I'm special. Waiting for someone to see it.Jack: *smiles* I saw it.
- All of "Exit Wounds". Just pick a scene.
- When Captain John Hart tells Jack, "I am sorry for your losses." Then he kisses Jack on the cheek and leaves. This man is a heartless, deceitful person, and yet he genuinely shows sympathy (or is it empathy?) for the man he claims to love. It's just so damn sweet.
- Toshiko's final message to the team.
Okay. So if you're seeing this I guess it means I'm well, dead. I hope it was impressive, not crossing the road or an incident with a toaster. I just wanted to say, it's okay. It really is. Jack, you saved me. You showed me all the wonders of the universe and all those possibilities and I wouldn't have missed it for the world. Thank you. And Owen...you never knew. I love you, all of you. And I hope I did good.
- The worst part about that being how she uses it to finally address Owen and give him her declaration of love. Only Owen's not there anymore, either...
- Even before that, with Toshiko's plea for Owen to stop shouting because "You're breaking my heart".
- Their entire conversation leading up to Owen and Tosh's deaths is heart breaking.
Owen: We never did get that date, did we, you and me? We sort of, uh, missed each other. Was my fault, didn't notice until it was too late. I'm sorry.Tosh: Me too.
- The episode's final dialogue—the "calm after the storm" moment when you realize just how much the events of the episode have cost the team:
Jack: Now we carry on.Gwen: I don't think I can. Not after this.Jack: You can. We all can. The end is where we start from.(Fadeout on Jack, holding the remaining members of his team close.)
- Children of Earth. God, where to start? Okay, Ianto's death's probably a good starter.
- Eugene Jones' funeral in "Random Shoes". Particularly when his father sings "O Danny Boy".
- Seeing who Owen was before Katie died, and comparing that with the bitter man he turned into afterwards.
- Poor Lynn Pierce in "Small Worlds" who not only lost her boyfriend Roy (he might be a jerkass towards her daughter but she did at least care about him at some point), but also her daughter Jasmine, who she still loved deeply despite her talking to "imaginary friends and acting somewhat strange, is taken away by the Fairies to become a Fairy herself with little hope of ever seeing her again. While giving up Jasmine helped protect the world as the Fairies threatened to cause major havoc on the world if they didn't get Jasmine, we are talking about a grieving mother who have to not only lose her boyfriend but forced to give up her only child with no real say in the matter. Her having emotional breakdown and attacking Jack is understandable as she pretty much lost everyone she loves on the same day.