Chimera Ant Arc

Series: Hunter x Hunter
Main Characters involved: Killua, Gon, Kite, Meruem, Pitou, Netero, Knuckle, Palm, Meleoron

Gon, Killua, and friends race to put a stop to the up and coming all-powerful chimera ant King and his royal gaurd. While this arc is not only a masterpiece, it is criminally underrated in the arcs in HxH. This arc has everything: action, drama, tragedy, romance, suspense, etc. This is one of the most suspenseful story arcs I have ever watched, I remember watching this while it was airing and being on the edge of my seat every week. It was masterful story telling and an arc I will always remember and admire.

Impel Down / Marineford Arc

Series: One Piece
Main Characters involved: Luffy, Ace, Buggy, Boa Hancock, Crocodile

A rescue arc featuring Luffy fighting desperately to save his brother Ace from his impending execution. He chases him from place to place, against all odds trying to save him. Filled with great fights and a lot of serious moments that were not seen in One Piece prior to this arc. Yet another one of my favorite arcs of all time.

Nadeko Medusa Arc

Series: Monogatari Series
Main Characters involved: Nadeko, Kaiki, Senjougahara, Araragi

Nadeko is back with a vengence and newfound god powers, set to kill her unrequited love and his girlfriend, and their only hope at survivng is their previous enemy, Kaiki! This arc is seriously a roller coaster and the fact that they had to rely on Kaiki is what plunged this arc into god-status for me. The stakes were at an all time high in the show and it was truly amazing. Definitely my favorite arc in the show, and the ending was a great payoff.

Ryoka Invasion Arc

Series: Bleach
Main Characters Involved: Ichigo, Rukia, Yoruichi, Chad, Uryuu, Orihime, Byakuya, Renji, Aizen

This arc features the invasion of the soul society by Ichigo and his friends, in order to save the shinigami who saved him, Rukia! It includes some of the greatest line up fights and slow build up of a rescue mission in a strange new world ~ This is one of the most memorable arcs in anime and is the greatest Bleach arc by far (and probably my personal favorite on this list).