Tom's Instruments:
Guitars:
<Tom's famous pawn shop guitar.  It has two volume and one tone control, with two pickups.   Some songs: Tire Me, War Within A Breath 
<The "Arm the Homeless" guitar.  Has a Kramer headstock, performance neck, two volume, one tone control knobs.  he keeps this guitar tuned standard (EADGBE).  Some songs: Bullet In The Head, Know Your Enemy, Fistful Of Steel, Bulls On Parade, People Of The Sun, and Vietnow. 
<A black american-standard telecaster. He always keeps this guitar tuned at Drop D (DADGBE).  Some songs:  Killing In The Name, Freedom, Wake Up, No Shelter, Testify, and Born of a Broken Man 
<One of Tom's newest guitars.  It is an Ibanez specialty hollow body, with two volume and two tone knobs, and six specialty knobs.  Song: Guerrilla Radio

 
Amp
<The sam amp Tom has used basically, forever.  Its a Marshall JCM-800 50-watt head circa 1987.

 
Pedals

Ibanez digital flanger used in: Guerrilla Radio, Wake Up, and Freedom.
DOD EQ: set flat so he can jump to 11
Boss DD-5 Digital Delay
DigiTech Wammy pedal used on: Know Your Enemy, Bullet in the Head, and Ashes in the Fall
CryBaby wah used in: Vietnow, Bulls on Parade, Guerrilla Radio, and No Shelter