Depends on the song when it comes to his basses. With Eb songs, he uses Warwick (with EMGs). With C# songs, he uses Spectors.
Also, if I were to guess, he runs a parallel rig. One Ampeg SVT set up clean with tons of low end, and another one with grit. I don't remember if he uses an MXR M80 or BDDI but since it sounds pretty dark, I'm going to assume it's a BDDI.
EDIT: That's actually how he runs his rig. Two SVTs set up to handle the massive low end (with 1x18' speakers), and two SVTs to handle the distorted grind (with 8x10 cabs). Watch them perform at Kimmel in 2014. You can see his cab setup; An 8x10 stacked on two 1x18s.
EDIT: Wait a minute... Holy poopie this is an old thread.