After recieving many requests for information of this nature, here is a listing of all known gear that Jun uses, along with additional details wherever possible.

Custom Guitars
Don Grosh Lipstick
ESP 82 Custom
ESP 82 W-Neck
ESP Horizon Custom
ESP Jasperwood
ESP KoaMaple (1996, Koa/Maple, 22 Frets, EMG SA-SA-89, Floyd Rose)
ESP No Fear
ESP Red Telecaster
ESP Roadrunner
ESP Sonic (1998, Given to Yuji Naka)
Fender Japan '58 Replica Strat
Performance Hawaiian Koa (Hawaiian Koa body, hard maple neck, PG-10H/SD, 22 frets)

Retail Guitars
Fender Musicmaster '64
Godin ACS Nylon Synth Guitar (Silver leaf maple body, mahogany neck)
PRS Custom 22, 10 Top
Spector Euro 4 Plum Stain Bass
Jerry Jones Master Electric Sitar (Masonite body, Indian rosewood neck, black gator finish, 21 frets)
Taylor 714CE Electro Acoustic
La Patrie Etude
Washburn Steve Stevens SS80

Amps
Line 6 POD Pro
Line 6 POD XT
Marshall (Unspecified)
Peavey 5150
Soldano SLO-100R
Soldano SP77 Preamp

Pedals
Digitech Whammy
Jim Dunlop TS-1 (Tremelo)
MXR Dyna Comp (Compression)
MXR Phase 90 (Phaser)

Recording Gear
Digidesign Pro Tools Rig
Logic (Sequencer)
Mackie Analog (Mixer & Studio Monitor)
Yamaha (Digital Mixer & Studio Monitor)

Other Equipment
Akai Sampler(s)
Alesis Sound Modules
Korg Synthesizer(s)