he'll have been using the Explorer, SG and that other hollow body thing with the diamond F-holes and strat headstock. Into a Recto and a Vox AC-30. All stock pickups.
On the 1st Foo Fighter's album Dave Grohl used mainly a LP and a Marshall JCM900 head and cab.
On 'The Colour And The Shape' (if I remember right) he used a Gibson Explorer, a Gibson RD and maybe a LP? I can't remember what amps though
On 'There Is Nothing Left To Lose' he mainly used a Gibson Trini Lopez, a Telecaster, a SG tuned to A (for Stacked Actors) and amps were a Vox Ac30 and a Mesa Dual Rectumfrier.
As for gear on 'One By One', I know when he toured the album he was using a Dan Armstrong Plexiglass guitar and Rectumfriers. I assume he was using his Gibson Trini Lopez to record the album too.
There may be some mistakes in my info, but as far as I remember, this is what I read in guitar magazines and interviews