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Tear Jerker: Switched at Birth
Bay and Regina's conversations about why Regina never contacted her. Not surprising given Bay's status as The Woobie
"But I was your daughter. Me. Not her, and you chose her over me. No. You knew? All those years you knew, you followed me and you never once came for me?"
"Painful for you, what about me? My whole life I've felt like I didn't belong, and I didn't know why, and I thought it was my fault."
Daphne's description of her relationship with Bay:
I don't know what she is to me. I don't know what to call her. I don't even know if I like her, but she is the only person in the entire planet that knows what I'm going through, and if I piss her off...
In Los dos Fridas, When Kathryn asks her mother why she is alienating Bay, she explains that it's because Bay isn't her DNA. She explains that she still loves Bay, but she can't help the fact that she sees her differently. And Bay overhears this in the next room.
The end of the prom episode. The devastated look on Bay's face after she finds out that Emmett cheated on her really makes you want to hug her.
Also the end of the Season 2 Finale, when Bay realizes that Ty cheated on her too and goes to Emmett and asks him, "Why do men cheat?". Even more so when Mary confronts Ty about this and realizes that he didn't really cheat, and he set it up so Bay wouldn't miss him if he died in war.
The end of the What If? episode, not only when Bay and Daphne find out Regina died on their birthday, but John also gets a heart attack shortly after that scene. The entirety of that episode, also constitutes as one because you see just how damaged Bay and Daphne's family were.
Toby and Nikki breaking up in The Ambush.
Probably the greatest tear jerker of all is Angelo's death in the Image Disappears.