Episode 12, "Homefront" could be considered this. It has several revelations. Cheshire is Artemis' sister, their mother was in jail, the conformation that their father is the Sportsmaster, the team almost dying, Red Tornado potentially betraying everyone. Artemis finally in school, two Batgirls popping up, Robin showing up in school and heavily implying that he's figured out Artemis' secrets...
Episode 16, "Failsafe" is a fairly major one and a major example of Nightmare Fuel - that the whole episode, an increasingly disastrous fight against an alien invasion was an unwinnable training situation that soon became real in the minds of Young Justice. Major Wham at the end.
Episode 21, "Image," reveals that Miss Martian is a horrible alien moster and her personality and appearance in her human form are based on a character from a sitcom she watched on Mars.
"Happy New Year", the first episode of Season 2. Three words: Five YearsLater
"Alienated": Aqualad is evil!
"Salvage": Roy and Jade got married, and have a daughter.
"Depths": Artemis dies...but then she doesn't! Aqualad isn't really evil, he's just a Reverse Mole under deep cover - and only Artemis, Wally, Dick and Kaldur know! M'gann and Superboy broke up because she tried to erase his memory of being mad at her for manipulating people's minds!
"Darkest": Kaldur explodes Mount Justice, and Wally starts to wonder whether he's truly a double agent or if he's truly turned.
Let's not also forget Jaime, Bart, and Garfield, are captured by Kaldur's team and it's revealed Scarab can take control of Jaime's body.
"Before the Dawn", anyone? If for nothing else, the revelation that the Blue Beetle is the villain in the future counts.
On top of that, Miss Martian comes across Kaldur whilst the team are rescuing their captured members, and proceeds to mind rape him in response to his killing Artemis, leading to her finding out that he's really The Mole & Artemis is still alive, leaving herself & Kaldur catatonic.
From "True Colors" Not only is Psimon going to be combing through Aqualad's thoughts, but the Light are aware of the runaways' location and want to form them into their own young team.
"Runaways" Blue Beetle's on mode, he and Green Beetle are moles for the Reach, and the kids are recruited by Lex Luthor.
"Summit: Aqualad and Artemis are exposed as moles...and then reveal the Light's duplicity, break the Light and the Reach's alliance, , incapacitate both the Brain and Black Manta (and possible Ra's, depending on how long it will take to get him up again), and get the Reach Ambassador removed from his position in addition to using the meeting to arrange an Engineered Public Confession that destroys the Reach's Villain with Good Publicity act. The Light just gained the War World and the Reach wants to destroy Earth.
"Endgame": Wally gets Killed Off for Real. The ending is a cliffhanger, in which Darkseid himself makes his Young Justice debut. Unfortunately since the show wasn't renewed for a third season, we're Left Hanging.