NOTE! I know there is a thread similar to this, but that setup thing was missing a few things. This thread is a corrected version of that thread.
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Tim Commerford's Setup
1992-1996
Basses 
-Music Man StingRay
-natural finish
-pickguard removed
-Rickenbacker 4001 (used pre-Rage Against the Machine)
Amplification 
-2 Ampeg SVT-2PRO Heads
-2 Ampeg 8x10 Cabinets (these were covered by an American flag that was burned often
Pedalboard
-Marshall Guv'nor Distortion
-MXR Flanger
-Dunlop Bass Wah
1996-2000
Basses 
-Fender Jazz Bass
-natural ash finish
-no pickguard
-one volume knob, one tone knob
-Tim rewound the pickups on that particular bass and had Fender Custom Shop make several more

-Fender Jazz Bass
-Sunburst
-Black Pickguard
-Bad Ass II Bridge

-Fender Jazz Bass
-Olympic White
-Read Tortoise pickguard
-Bad Ass II Bridge
-Fender Jazz Bass
-Black
-Red Tortoise pickguard
Amplification
-2 Ampeg SVT-2PRO Heads
-2 Ampeg 8x10 Cabinets
Pedalboard
-Dunlop Bass Wah
-Boss OC-2 Octave
-Boss DD-3 Delay
-Homemade Overdrive (made from a broken wah)
-Custom ABY Amp Selector
-Aphex Punch Factory
2002-2006
-Same basses used from 1996-2000

-Fender Jazz Bass
-Natural Ash
-Tortoise Red Pickguard
-Pickup Selector
-Gotoh Bridge
-It appears the pickguard was cut so he could put the thumb rest on easier
-White Fender Jazz Bass
-Red Tortoise Pickgaurd
-Tuned BEAD
-Bad Ass II Bridge

-Black Jazz Bass
-Mirror Pickguard
-Bad Ass II Bridge

-Fender Jazz Bass
-Black
-Red Tortoise pickguard
-Left-handed Precision Bass neck (so the B string would be tighter)
-Tuned B-E-A-D
-Bad Ass II Bridge

-Fender Custom Shop Double Neck Bass
-Cherryburst
-One neck tuned E-A-D-G, the other tuned B-E-A-D
-Never been used live

-Custom Ovation Acoustic Bass
-24 Fret Neck
Amplification 
-Ampeg SVT-2PRO Head (Distortion)
-Ashdown ABM 500RC EVO (Overdrive)
-Mesa Boogie M-Pulse 600 (Clean)
-Ampeg 8x10 Cabinet
-2 Ampeg SVT 4x10 Cabinets
[center]Pedalboard

-2 Dunlop Bass Wahs (one for the clean channel, one for the distortion channel)
-Aphex Punch Factory
-Homemade Overdrive Pedal
-Custom ABY Amp Selector
-Boss OC-2 Octave (the picture above doesn;t show this pedal)
2008
Basses 
-Lakland Joe Osborn
-Sunburst
-Pearloid Pickguard

-Lakland Joe Osborn
-Natural Ash Finish
-Maple Inlay Fret Markers

-Lakland Joe Osborn
-Sunburst
-Red Tortoise Pickguard

-Lakland Joe Osborn
-White Pickguard
Amplification 
-2 Ampeg SVT-VR heads
-2 Ampeg 8X10 Cabinets
Pedalboard
-Same as the 2002 era pedalboard, except one wah instead of two
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Miscellaneous
Thumb Rests
-Tim has custom (or homemade) thumb rests on all of his basses. They're long and skinny, and fit in between the jazz bass pickups
Strings
-Tim is an endorser of Ernie Ball Strings
Bass Detuners
-Tim has been known to put Hipshot Bass Xtender on some of his basses
Straps
-Tim uses custom Levy straps that fit around his entire houlder rather than just the clavicle
Strap Locks
-Tim uses Grolsch rubber beer bottle tops as strap locks
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More Bassists's rigs to come, leave comments and request bassist's setups please!