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Tear Jerker: Dollhouse
Joel Mynor and his wife Rebecca (imprinted into Echo) in "Man on the Street" (1x06), especially the end of that episode, when he gets to welcome his "wife" to the new house she never got to see (the real Rebecca died in a car crash on her way there). He's a creep, but he's a sweet creep.
Echo, in her supposedly inactive persona, choosing to be sent back to Joel to complete the engagement. Brings a whole new dimension to her joy in the final scene.
Revisited at the end of "A Love Supreme" (2x08) when Echo becomes "Rebecca" once more, to give Joel "her" blessing to remarry.
The scene that shows Boyd leaving in Epitaph One.
In "Needs", the scene that shows Sierra and Victor promising to find each other no matter what happens, November weeping at her daughter's grave, and Echo leading the Actives above ground. The latter not so much sad tears, but more from the beauty of the scene.
Paul's brain-death, straight after he and Echo fell in love with each other.
The scene in "A Spy in the House of Love" (1x09) Mellie/November, in Manchurian Agent mode, tells Paul she's an active.
Speaks-through-November: I have a message for you from inside the Dollhouse.
Paul: This isn't funny...
Speaks-through-November: My name is November.
Paul:Mellie. Your name is Mellie.
Speaks-through-November: I knew this would be hard for you to hear.
Paul: If you're pissed I'm still investigating the Dollhouse-
Speaks-through-November: This body belongs to a doll.
Paul: -just tell me. Don't do this.
Speaks-through-November: I'm sorry we had to deliver the news to you like this. In this body. The Dollhouse is likely to discover we've been placing messages in their imprints; this is the only way we could talk to you.
Paul:[shaking his head] They did this to you...
Speaks-through-November: They did this long before you knew me. They've been using this body to spy on you for months. The only reason Mellie exists is because of you.
Paul: Aren't I special?
And when she goes back to normal... Ouch. "Then why aren't you kissing me?"
At the start of "Stop-Loss" (2x09), Adelle brings back Roger the night before Victor is to regain his freedom as Anthony, but Roger spurns her because he loves another (Sierra), then assures Adelle she's "too good" to need to bed an Active. Adelle breaks down sobbing.
The end of "Haunted" (1x10), when Margaret-in-Echo prepares to have her imprint erased. She asks if she will see her whole life flash before her eyes, and Adelle has to watch her friend die for the second time - and starts to cry as the wipe begins.
Margaret was literally within arm's reach of her beloved husband Jack - but, poignantly, could never tell him so because she couldn't blow her cover. (Though she slipped once - after Jack was wounded helping to take down her murdering son Nicholas, Margaret instinctively ran to him and shouted "Darling!" before catching herself.)
"Haunted" also has the moment when Margaret's daughter talks about growing up with a cold, unaffectionate mother who suddenly shows love towards someone else.
The sheer joy in her face when Echo!Margaret is riding her horse again.
Claire confronting Topher about her being an active, toward the end of "Omega" (1x12): "I don't see why it was so important for me to hate you." Not to mention, Topher sounds on the brink of tears for the whole of the ending montage.
In the episode "Haunted", when Topher borrows Sierra for a "diagnostic check." He implants in her the personality of a fellow geek. But it's at the end of the episode when it's revealed he did so to have someone to celebrate his birthday with...
And at the end it turns out that Adelle knows he's doing this, but lets him anyway, essentially to keep him sane.
Her voiceover at the reveal is heartbreaking.
Adele: "Loneliness leads to nothing good. Only detachment. And sometimes the people who most need to reach out are the people who are least capable of it. In any case, it only happens once a year."
Future!Topher's breakdown in "Epitaph One", as Adelle hugs him and tells him it's all right. "I know what I know, I know what I know, I know what I know..."
Whiskey: "Was I my best?" Caroline-in-Iris: "Better."
What makes this so sad is that it follows directly after the episode where Doctor Saunders found out she was actually an imprinted Whiskey. In that episode, her refusal to freak out or start doubting herself was nothing less than a Crowning Moment of Awesome, so seeing Whiskey back in that blank Doll state is crushing.
Hell, "Epitaph One" was basically a tearjerker from when Caroline woke up in the little girl's body until the end. Her getting all excited to see Claire Saunders and finding out it's Whiskey instead. "Was I my best?" That gorgeous song played over the last few minutes. Whiskey refusing to leave and then just sitting down and letting herself be gassed with the bad guys. Caroline's summation of the apocalypse: "Kids playing with matches. And they burned the house down." The Remembrance Wall and the pictures of Victor, Sierra, November and Echo. And finally, Caroline and the surviving rebels climbing the ladder and hoping it will lead them to Safe Haven, and that it still is a safe haven.
Caroline-in-Iris looking at the picture of her own body, not knowing if it's even still alive...
Vows. If you get through Claire's incredible amounts of bitterness and pain in her scene with Boyd, then don't worry, there's still her and Topher having near-simultaneous, award-worthy complete breakdowns from guilt and self-hatred...
"Why shouldn't I love you? Aren't you lovable?! Aren't you Big Brother? Aren't you the Lord my God?! Why should I fight your divine plan?"
Opinions vary on whether the episode was amazing or unoriginal and melodramatic, but dear God "Instincts." If you weren't sure how you felt about what the Dollhouse was doing, this episode should probably help you decide.
"Belonging". Pretty much everything about the Sierra/Priya storyline. And Topher was heartbreaking too.
Priya: "This secret we have... can you keep it?"
Topher: "I can keep it. But I don't know if I can live with it."
Priya: "I know I can't. But I don't have to."
Not to mention Sierra, after being wiped again, smiling innocently - with Priya's last tear still on her face.
The very beginning of "Belonging"—Topher crying and saying something along the lines of "I only wanted to help her!"
Echo seeing Victor, who had told Sierra he'd 'wait right here' for her until she got back, sitting in the same location - not realizing that Sierra was gone permanently.
"Getting Closer": Topher seems like he's finally happy, Saunders comes to talk with Bennett for a moment in what seems like a Pet the Dog moment... and then she shoots her in the head just as Topher comes back into the room. Topher's Heroic BSOD doesn't help.
His subsequent conversation with Ivy, especially considering their relationship thus far and the fact that we don't know what happens to Ivy after this, is part this and part Crowning Moment of Heartwarming.
Topher: I got it from here. You take your chance, you slip out. In the real world, you can write your ticket any place you land.
Ivy: I really do want to help you.
Topher: Then live! You have a remarkable brain. I think it should stay in your head. Ivy, don't become me. Go. Go!
"The Hollow Men": Even Caroline was crying when she sent Boyd to his death.
Mellie's suicide. Especially her turning around so Paul wouldn't see her crying.
The end of "Epitaph Two: Return," particularly Topher's Heroic Sacrifice, and Echo "reuniting" with Paul. Before that, Echo's tirade toward Priya for avoiding Anthony and its segue into her own total breakdown over Paul's death, and her regret for not fully showing her love for him while he was alive.
Five words: "Your job is way harder."
Eight more words: "I don't want to cause any more pain."
And for some happy tears, try the scene immediately after the Echo-Paul moment, when we see Priya, Tony, and their son together as a family. Having the parents give little Tony one of the children's books they used to read when they were dolls is a wonderful touch, indeed a taste of Fridge Brilliance.
Saunders killing Bennett.
Rossum and Senator Perrin betraying Madeleine at the end of "The Left Hand" by "proving" that she was mentally unstable and that her memories of the Dollhouse were actually the result of brainwashing, and that instead she was in a psychiatric hospital for three years.