Mahou Sensei Negima! has one hell of a wham episode when the Ala Alba are on a trip to the magical world. They arrive in the magical world, and it almost seems like a vacation... until the big bad shows up, stabs the hero through the chest, and beats the crap out of everyone. Then he scatters the entire team across the entire magical world, many into wilderness they're ill-equipped to survive. (Oh, and gets them blamed for his attack and hunted as wanted criminals.)
Pretty much everything that happens for the first few times Kurt Godel is around. Let's see: reveals the identity of Negi's Missing Mom and the fact that said Missing Mom is widely (but falsely) believed to be responsible for a genocide, claims to be The Man Behind the Man who's responsible for pretty much everything bad that's ever happened to Negi, and triggers Negi's Superpowered Evil Side, almost getting our beloved Wide-Eyed Idealist to kill him in cold blood.
In chapter 311, Chachamaru seemingly blows up Fate. But remember how Fate is the 3rd in the Averruncus series? Numbers 4,5, and 6 crash the party, and they make him look as gentle as Nodoka.
Does anyone remember the first anime? The episode where Asuna drops dead counts. And the following episode, where it actually manages to get worse. Much worse. They even dropped the cheerful intro, just in case you hadn't caught on yet.
In chapter 329, Fate stops fighting and agrees to work with Negi. Then the Lifemaker makes his entrance by shooting them both. Then in chapter 330, it's revealed that ALL of Cosmo Entelecheia has been revived... even the ones that died twenty years ago.