In "The Test", Steven begs the Crystal Gems to make a challenge for him to go through. While he passes through Garnet's room, a wall of flame she set up starts and then retracts before he crosses it, giving viewers a few seconds to pick up that the tests were rigged to let him succeed before it becomes obvious to Steven.
In "Jail Break", Sapphire addresses Steven by name, even though he hadn't told it to her. Shortly thereafter, Sapphire and Ruby fuse into Garnet.
In "Keystone Motel", right before Sapphire and Ruby's argument about the events of the previous episode ("Cry for Help") gets to the point where they de-fuse, Garnet gets twitchy and her hands start moving independently.
In "Message Received", Steven locks Peridot in the cab of the barn's pickup truck because she was planning to contact Yellow Diamond. While Steven and the Gems are discussing what to do with her, you can hear her futilely mashing the truck's horn in the background trying to get out... until near the end of the conversation when the honking suddenly stops, indicating that she's finally figured out how.
In "Steven's Dream", Steven has a dream of giant palanquin, belonging to one of the Diamonds, so he and Greg go to Korea to find it. When they do, they find Blue Diamond's palanquin, except it's in perfect condition, while the one Steven dreamed of was in disrepair. Just behind some bushes is Pink Diamond's palanquin... and Blue Diamond.
In "Jungle Moon", the music changes to make use of a certain variation of the Diamond Authority theme when Stevonnie starts arguing with Yellow Diamond, hinting that they are actually dreaming as Pink Diamond.
"A Single Pale Rose" is one of the series' biggest Wham Episodes. There is a fair bit of this trope leading into the big revelation: namely, that Rose Quartz is Pink Diamond.
Every time Steven descends a layer into Pearl's mind, she has more and more pink in her design. She was Pink Diamond's Pearl, after all.
In the penultimate flashback, after the "shattering" of Pink Diamond, the crying Rose's skin is unnaturally pale, a hint that she's actually a shapeshifted Pearl.
When Steven enters the final flashback, he's sitting on the throne of Pink Diamond's palanquin.
The very fact that Rose Quartz is inside Pink Diamond's palanquin at all, despite her status as a wanted criminal. It was even a plot point in "The Trial" that it would be nigh-impossible for Rose to sneak up on Pink without a huge ruckus as there were no Rose Quartzes in her entourage.
When Pearl asks Rose if there's any way out of this mess, Rose refers to the supposedly uncaring Diamonds as simply "Blue" and "Yellow". The Diamonds themselves are the only ones who usually address each other on a First-Name Basis.
Pearl tells Rose that if they go through with what they're planning, Pearl's "purpose" (as Pink Diamond's servant) and Rose's "status" (as Pink Diamond) won't matter anymore.
Rose says "If this is really my world, I want to give it to the Crystal Gems." Earth was Pink Diamond's first and only colony.
When Rose starts shapeshifting, the Diamond synth plays.
In "Reunited", Steven weeps Tears of Joy at Ruby and Sapphire's wedding — but the tears won't stop coming. Cue simultaneous Oh, Crap! from Steven and Garnet as they realize that Blue Diamond, who has an empathic link with Steven, can't be far away.
