Noir Sam and the whole interrogation part in "They Stole Max's Brain!" Especially when you use Noir in the right moment with Skun-ka'pe's Minion.
Max managing to defeat Sammun Mak... using the salutes and oaths that Sammun Mak himself created!
Three words. MAX VERSUS CHARLIE HO-TEP. (All right, four words.)
Some more words: of all the episode endings and final confrontations Telltale has done so far, this is just the most epic in its presentation (and still one episode in the season to go). Compared to the final encounter of the 2nd season where you banish the Soda Poppers in a pedestrian looking office with the Granny Weatherwax theory of witchcraft ("use whatever's handy even if it's not very impressive, it'll work just as well") you have Max, glowing with the Power Limiter off, in the sky, amid swirling winds, above the demonically-twisted Statue of Liberty locked in psychic battle, with the Sam clones marching in rows to their doom below, set to spooky chanting and organ music, with Sam below trying to help in any way possible.
Sal's Heroic Sacrifice. It turns out that the concept of cockroaches being immune to radiation was an Urban Legend, but Sal knew this anyway. He just figured that if his last act could be used to do some good, his death wouldn't be in vain.
If you try to shoot the Narrator in 305, instead of making an excuse about why he can't use his gun like he normally would, Sam whips it out and aims. The Narrator assumes he's bluffing and laughs it off, asking if he really wants to fire a gun in his partner's mind. Sam responds by pressing it to his forehead, finger on the trigger. They both stare at it for a moment before the Narrator snaps, "Okay, really, Sam, cut it out" and Sam puts it away, smirking.