Alabasta due to the scale of the conflict and interesting plot of it's antagonist working from the shadows to create a civil war primarily through intellect rather than power and it being one of the few cases where Luffy didn't get by due to brute strength or a power up. Summit War comes as a close second due to the permanent repercussions it had on the story and it's characters, though is held back from taking the top spot due to most of the potential quality that could've come from it's build up of future events being squandered almost immediately (eg. Luffy seeming like he'd get character development, only to completely regress to his old self by the next arc.)
Many will choose CP9 as a top contender, but I'd say it's average at best due to it's asspull power ups, ridiculous plot armouring that makes Pell's survival look reasonable and the character development it seemed to set up for Usopp and Luffy being completely erased by it's conclusion.