http://www.youtube.com/watch?v=9UMzuJFNg38&feature=player_embedded
Guitars
Josh uses a core of Strats, starting with Chad Smith's '63 Tobacco Sunburst used for older songs like "Higher Ground" and anything with a whammy bar. His main Strat is a black '66 with a '68 neck and he also uses a black 1974 hardtail Strat as his backup. He uses a Gretsch White Penguin for Californication-era songs as a tip-of-the-hat to Frusciante, an early-70s Gibson ES-335 for "Universally Speaking" and a Neil Young song, a '67 Telecaster that was a gift from Frusciante long ago, a '64 custom-color Fender Jaguar used for lighter songs, a 12-string Gibson Firebird with some modifications to the pickguard and switching, a Fender Coronado 12-string in burnt orange (dropped a half step for "Breaking the Girl"), and a "Fools Telemaster" relic'd Tele/Jazzmaster-style hybrid. He uses D'Addario .010 - .046 on all of the guitars except the White Penguin, which is strung with .011 - .049. He uses Dunlop Tortex .60.
Amps
Josh Klinghoffer uses a three-amp setup. The vintage Marshall Major provides the basis for his tone with an emphasis on low-end, the Silvertone is run a bit quieter for midrange, and the Fender Super Six is set even quieter and provides top end. All three amps are on at the same time and the effects are run through all three.
Pedals
Josh changes his pedalboard setup constantly, but when we caught up with him, it'd been steady for a few shows. Certain pedals are on the board to capture the recognizable recorded tones, while others are used for fun as he feels in any given moment. The signal comes into a Boss TU-2 tuner, into an Ibanez WH10, Keeley-modded Boss DS-1, Marshall Guv'nor, Pigtronix PolySaturator, Wilson Effects Fuzz, Boss Analog Delay, Boss DD-3 (clipped repeats), Boss DD-3 (glitching Radiohead-style), Electro-Harmonix Deluxe Memory Man (short slapback), Electro-Harmonix Deluxe Memory Man Tap Tempo (used with the expression pedal), Boss Vibrato ("Suck My Kiss"), Boss CE-2, Boss CE-2 (modded for wider sweep), Lastgasp Labs Cybertronic (high-end, whispy filter), Moog Moogerfooger Low-Pass Filter, Line 6 FM4 (synth sounds), Moog Moogerfooger 12-Stage Phaser (used for "Throw Away Television" in conjunction with the FM4's sequential synth), Boss SG-1 Slow Gear, Boss RV-5, Electro-Harmonix Cathedral, Electro-Harmonix Freeze, Boss DD-6 (cascading repeats), Electro-Harmonix Goly Grail, Xotic Effects EP Booster, Wilson Effects Haze, Lo-Tech-N-Fi-Bot Pocket Synth, Line 6 DL4 (used as a looper and phrase sampler between songs), Bright Onion looper (used as a kill switch), Boss CS-2 Compressor, and a Framptone 3-Banger amp switcher.
The pedals are wired into a Bright Onion Pedals switcher that allows Sheppard to bypass an entire board or each individual pedal in case of a problem, as Josh is fairly rough when kicking his pedals on and off.