1960's Fender XII
1960's Fender RI Telecaster custom
1970's Fender Telecaster (blonde, black)
1980's Rickenbacker 360 6-string (jetglo and walnut)
1990's Rickenbacker 360v64 (fireglo)
Rickenbacker 330 6- and 12-string (jetglo and natural/mapleglo)
Rickenbacker 370/12 - Roger McGuinn model
Danelectro 12-string (blue sparkleburst)

Danelectro 12-string (burgundy sparkleburst)
Danelectro
Rickenbacker 340
Gibson Country Gentleman
Gibson SG
Gibson Les Paul
Gibson 'Flatiron' F-style mandolin (tobacco sunburst)
Gibson jumbo acoustic
Gretsch
Guild jumbo acoustic
Paul Reed Smith
Jerry Jones electric sitar
Fender JagStang [Kurt Cobain's] (also played by Mike Mills)

Taylor 610 Jumbo acoustic (see: Daysleeper video)

amps:
early gigs - i've heard he ran a lot of his guitars through a Fender Bassman 60w or 100w to get that nice clean, jangly sound
Fender Twin
Vox AC-30
Marshall AVT(?) stack
Mesa Boogie (w/built in tremolo)

pedals:
Big Muff Pi (large green pedal, nicknamed Sputnik by Pete himself)
Pro Co Rat
wah pedal
various other pedals, filters, rackmounts, but don't forget the traditional tape loops and studio effects that contribute to the album material

other:
E-Bow Plus
various slides

Rickenbacker 360 strings:
these are individual Dean Markley strings and quite the heavy gauge, sometimes referred to as telephone wire gauge
.013 Plain- Swedish Steel
.017 Plain- Swedish Steel
.026 Wound- Nickel Steel
.036 Wound- Nickel Steel
.046 Wound- Nickel Steel
.056 Wound- Nickel Steel

Peter also played drums on the untitled 11th track on Green and not to mention has played piano/keyboard as well, such as during early gigs as seen on the sleeve of Reckoning and in Road Movie.