On the album "Black Holes and Revalations" the song "City of Delusion" has a really cool filter sweep effect in it.
-one with an envelope that swells accross sevral bars of the song.

Anybody know what was used for that? have you seen him perform this live?

I imagine It was done with a footpedal controller of some kind...

It's always kind of a mystery as to how -precisely- he gets his sounds, but I believe that he gets many of his tones from rackmount effects nowadays. He uses a Line 6 POD and I know he uses a Big Muff. In terms of other pedals, I've heard he has some Boss and Line 6 equipment, or at least has in the past. He also has an Akai Deep Impact.