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Jack's pretty good at making people tear up. Go back to season one, and the scene where he shows up at Sydney's house on Thanksgiving and gives her the file clearing him of spying for the KGB (the irony being that it's Sydney's mother who was the KGB agent). He's practically tearing up himself as he confesses he might not have been the best father, but he would never want her to believe he would put her or his family in danger.
Francie's death. She may have been the scrappy to a lot of people , but seeing her dead in the kitchen of her own restaurant brings tears to your eyes. It gets worse in season 3 when Alison Doren (Francie's double and the woman who killed her) returns, and we have a flashback to the murder. Francie is alone in the restaurant talking to her her mom on the phone, clearly happy about how business is going, when she hears a sound behind her. She tells her mom to hold for a minute, turns and sees her double with a gun pointed right at her. All she can say is, "You're me" before she is told to back into the kitchen, where she is promptly shot. Alison then picks up the phone and says: "Mom, I'm going to have to call you back". It's pure nightmare fuel.
The scene between Jack Bristow and Elsa Caplan in Season 2's "Endgame". Elsa Caplan is a Russian spy who was tasked with marrying scientist Neil Caplan. Thinking she is as duplicitous as Irina Derevko, Jack spits insults at her, eventually promising that she will "never see [her] child again." Elsa shouts "Don't you dare take my son away from me! Don't you dare—!" before bursting into tears. It's heartbreaking and very real, and Jack is stricken speechless by his realization that she deeply cares for both her husband and child.
Emily Sloane: The scene in "Almost Thirty Years" where she drinks the wine, her betrayal of Sloane, then her almost-escape and death scene in "Truth Takes Time" and the scene in "In Dreams" when Jacqueline's death is revealed.