The first half of "The Fall" is just one long Awesome Moment for Hardy, as he manages to completely destroy the bond between Emma, Jacob, and Paul just by sitting there and making observations. Just the simple fact that Ryan Hardy is in the farmhouse is enough to make Jacob wet himself.
Mike Westen's reaction to being kidnapped and interrogated/tortured by Roderick and his crew. Despite being literally beaten to death by degrees (and eventually stabbed), he refuses to give up Claire's location.
Claire beating the crap out of Emma and threatening to kill her if she ever goes near Joey again.
From the same episode, her mocking of Joe's previous failure as a writer. To his face.
Joe: You shouldn't have read that, Claire.
Claire: Believe me, it wasn't easy. I guess you didn't learn anything from your last book.
Claire racking up more awesome points, by way of stabbing Joe in the gut by pretending to give in to his romantic advances.
Claire going for three episodes in a row of awesome, by cracking Joe over the head with a bottle of wine, and stabbing his stitched up stab wound with a dinner fork. And then Kicking The Son of A Bitch
This all summed by the following dialogue:
Emma: What happened!?
Joe: Claire did!
Ryan telling off Joe, when he confronts him at the lighthouse.
Ryan: I am so bored with you. I am so bored with you, and Edgar Allen Poe.
Joe meeting the end he so richly deserves, courtesy of an exploding boathouse.
Season 2's reveal that Joe had planned to fake his death all along by swapping himself with the corpse of his long-lost brother who matches him genetically. Damn, talk about Crazy-Prepared.
Lily Grey tricks Ryan and the entire FBI into thinking she's a helpless victim just so she could string along and manipulate Ryan's emotions. Oh yeah, and she has her own clan of psychopaths at her disposal, including the two men who "attacked" her, Mark and Luke. She's basically set up as Joe Carroll's perfect Distaff Counterpart.
Ryan and his team manage to make a serious dent in the "International House of Psychos" over the course of just two episodes. Granted, they were aided by Joe's sudden betrayal, but killing off three of Lily's "children" and putting her favorite in the hospital (and convincing her that he's dead, too) is no small feat.
Weston killing Lily. Some people felt that it was a case of They Wasted a Perfectly Good Character, but DAMN if Weston wasn't badass about it. Plus, the look on Lily's face was epic when it was obvious where it was going:
Hardy's infiltration of the Korban compound at the beginning of "The Reaping" evokes "The Fall" from the first season, as he sneaks around like Solid Snake in total control of the situation, only getting captured when he wants to be, in order to get a face-to-face with Joe and unbalance him.
Claire finally ends Emma.
Kingston Tanner kills himself rather than give Joe Carroll the satisfaction of turning him or his son into a murderer. Joe's vain attempts to spin it afterwards are hilarious; once again something has not gone according to plan, and the Wannabe Chessmaster has no idea what to do.
Max pulling a Big Damn Heroes twice in the S2 finale, the second time she kills Luke.
Ryan refusing to kill Joe in the S2 finale feels like one. He refuses to play Joe's game, and it causes Joe to have anotherVillainous Breakdown.