From "Bismuth", we have the revelation of exactly what led to Bismuth being bubbled:
Bismuth: That's exactly what she said.
"Steven's Dream", immediately after the Wham Shot of Blue Diamond's palanquin:
Blue Diamond: Poor Pink...
Scenes with series-wide implications:
"Ocean Gem": "All those monsters we fight used to be just like us!"
This line from "Island Adventure" casts Lars and his actions (from both before and after this episode) in a very different light.
Lars: Sadie, do you ever get lonely... Even when you're around people?
The appearance of a Homeworld Gem in "Warp Tour" is treated with the gravity it deserves, but one specific line drives home how much of a Very Bad Thing it represents:
Pearl: They're coming back. I can't do this! Not again!
In "The Return", Greg hints at the Gems' deepest regret, and how they don't want Steven "thinking of them like that". Steven presses the issue further:
Steven: Like what? ...Dad, like what? Greg: Like aliens, Steven! Aliens who invaded Earth!
Yellow Diamond: What do YOU know about the Earth?! Peridot: Apparently more than you, you CLOD!!
From "Alone at Sea", we have this line from Lapis during a discussion of Jasper:
Lapis: I miss her.
From "Earthlings":
Jasper: I've been fighting from the second I broke from the Earth's crust, because of what you did to my COLONY! Because of what you did to my PLANET! Because of what you did to my Diamond!! Steven: Y...Yellow Diamond? Jasper: Wha-?! My Diamond! Your Diamond! PINK DIAMOND!!
From "Back To The Moon":
Eyeball: I was there. I saw it with my own eye. I watched the leader of the Crystal Gems, Rose Quartz, shatter Pink Diamond!
From "Bubbled":
Steven: But did mom really do it? Did she really shatter her? Garnet: She had to. The Earth belonged to Pink Diamond. Destroying her was the only way to save the planet. For Amethyst to be herself, for Pearl to be free, for me to be together. For you to exist.
From "The Trial":
Steven (about the weapon used to shatter Pink Diamond): I probably had to use the "Breaking Point" to do it. Blue Diamond: IT WAS A SWORD!!! note Rose's sword is specifically made to always poof, never shatter. This is the first hint that there is way more to this story than it seems.
In the same episode, once Defense Zircon realizes there are too many holes in the official story of Pink Diamond's death for it to make sense.
Defense Zircon: No, whoever did this was already close to Pink Diamond. [...] and someone with the authority to cover it up afterwards! Someone with supreme authority, someone...like one of you! (points the Diamonds)
From "Jungle Moon":
Yellow Diamond: Then why don't you act like it, Pink?!
From "A Single Pale Rose":
Rose Quartz (actually Pink Diamond): I can't exactly shatter myself.
From "Change Your Mind", which is literally a wham line in how forcefully the character says it, plus it bluntly puts to rest the question of Steven's true identity:
White Diamond: What is this? Where is Pink? Pink Steven/Half-of-Steven:[monotone] She's gone. White Diamond: What did you say?! Answer me!!! Pink Steven:[Suddenly Screaming] SHE'SGOOOOOOOONE!!!!!! (A crater forms in the floor, and the walls of White Diamond's Sanctum crack from the scream.)
the character says it, plus it bluntly puts to rest the question of Steven's true identity:White Diamond: What is this? Where is Pink?