I'd like to see Sandman's daughter die because he couldn't get the medicine he needed for her, and in turn he can't think of anyone to blame it on except for Spider-man, so he is the one who comes out to reunite the singularly defeated bad guys under their new unseen leader, the so called "Master Planner" (name might be a little cheesy actually...) and their unknown financier...Otto Octavius and Norman Osborn! We thought they were dead, but Otto's legs crawled him up out of the water to safety and resuscitated him! He has some harsh amnesia and keeps getting flashes of memories that only make him angrier. And the Goblin formula worked some preservation and healing factor magic and voila!
Green Goblin (in a sicker suit. Make it a little more scary looking, almost zombie-esque perhaps, keeping with his "risen from the dead" motif)
Doc Ock
Sandman
and whichever 3 bad guys Spidey fights, locks away, and Sandman subsequently breaks out (I vote for Electro, Scorpion, and either Shocker or Vulture. Lizard has to much of an emotional attatchment. He's not as much a bad guy as he is like a werewolf type thing. Someone who doesn't want to hurt people, but can't stop himself. I can't see Connors conspiring with the S6, and definitely not Lizard, as he should be an inhuman beast who at best mutters what could be considered singular words and noises)
VS
Spidey and Black Cat!
Play it out like the last part of Mark Millar's "Marvel Knights Spider-Man", only it's 6 instead of 12, the Avengers don't show up!
They could even use that same storyline: 6 of Spidey's deadliest enemies have returned, some from the grave, to enact their revenge...and they know who he is, who he loves, and how to hit him where it hurts the most. Peter is so concerned about them coming after MJ that he forgets to keep a better eye on Aunt May. They both end up getting kidnapped and Peter enlists Felicia to help him in his biggest battle yet.