These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Tear Jerker: the end of "The Honeymoon," with Callie intentionally shoplifting food from a convenience store in order to get arrested. The utter lack of hope in her eyes as she eats a candy bar while crying is devastating
Callie and Jude's biological dad signing away his parental rights so they can be adopted by Stef and Lena, even though he wanted to be able to be their father again, because it was the right thing to do
"Adoption Day" gives us a slightly less Tear Jerker scene when it's revealed that Callie's biological father is someone other than she thought, meaning she can't be adopted until it gets sorted out. It's mitigated by a pep talk by Rita to not despair, Stef's assurance to Callie that they're not going to give up on her getting adopted, and Jude getting adopted (even though he said he didn't want to if Callie wasn't)
When Lena loses her baby. The emotional reaction from her and the rest of the family is just heartbreaking.
What an Idiot: Pretty much everyone in the third episode of the second season, Brandon decides to invite a few people over to hear their band. Mariana decides to invite her dance friends, who she knows will invite other people, but that's not her fault. Brandon instead of realizing this could get out of hand, decides "Sure, why not". Even after all the disastrous parties from the last season, nobody sees a problem with this party except Callie. Predictably, things go bad, people are trashing the house and they break the big living room window. Brilliant.
The Woobie: Callie and Jude, especially as we learn more about their backstory. Jesus and Mariana to an extent, though they've mostly grown past the stage in their life where they're as vulnerable.
Jerk Ass Woobie: Becka, one of the other girls at Girls United, is the most consistently antagonistic, particularly towards Cole, who she feels is just begging for attention (rather than being trans). However, she like all the other girls has a tragic backstory, and one of the webisodes reveals she's been cutting herself
After getting herself together with her mom getting rid of a crappy boyfriend, Becka finds out her mother has another new man. The look of fear on Becka's face says it all. She nearly burns the house down with everyone in it.
Gabby, another of the Girls United girls, is also abrasive and liable to make cruel remarks (although she's less transphobic than Becka). She also has an abusive father, a bad past involving being in a gang, and as the webisodes reveal she's HIV positive