There are only two things in my mind that qualify here: The Michael Hayes racist story, and the Jeff Hardy story. The Michael Hayes story led to Mark Henry becoming the ECW champion. It also led to Shelton Benjamin getting hte US title, and I think also Kofi Kingston the IC title. The WWE at least showed that this wasn't what the company was, and tried to make up for it. Shocking story, with some shocking results as well.
But Jeff's story was tragic. He's lost his home and all his possessions, and to top it all off, he's suspended as well. It must've been a really hard time for Hardy, and I think the wrestling world was feeling his loss a bit as well. And this had more influential consequences such as Punk winning MITB and the WWE title, as NoFate said. This story was overall more shocking, and had more of an effect on the WWE and the WWE's fans. Hardy gets my vote here.