Basses:
2 Wal Mach II 24-fret 4 strings w. birdseye maple facings (main basses)
1 Wal Mach II 24-fret 4-string w/ birdseye maple facings and greenburst finish
1 Wal Mach II fretless* w/ American walnut facings (used on Lateralus track)
1 Ernie Ball/MusicMan Stingray w/ tobacco sunburst finish and rosewood fretboard ( used with Peach, and on Tool tracks H., Forty-Six and Two, and Led Zeppelin cover No Quarter)
Amps/Effects:**
Mesa/Boogie M - 2000 Tube/S.S. Head
Mesa/Boogie Road Ready 8x10 cabinets
Demeter VTBP-201S Preamp
Tech21 SansAmp Bass Driver D.I.
Digitech Bass Whammy
ProCo Rat Distortion (modded for bass)
Boss GEB-7 Bass Equalizer
Boss DD-6 Digital Delay
Boss BF-2 Flange
Boss CEB-3 Bass Chorus
Accessories:**
Ernie Ball strings
Dunlop picks

*: It does not specifically say this bass is fretless, but I feel it is safe to assume that it is.
**: These sections are inherently hard to keep up with, so forgive any slight inaccuracies.