Jonny favors to use a rewired 90s Tele Plus armed with lace sensors and a cut off switch (he uses a single blue lace sensor at the neck, and he uses a humbucker of 2 red lace sensors at the bridge).  He also has various other Telecasters including older models and more of the same.  He sometimes uses a 1975 Fender Starcaster (Subterranean Homesick Alien).

Jonny's Tele with the Astroboy sticker.
 

Fender Twin Reverb
(click to enlarge)

Jonny has often said that he doesn't really care about the equipment he uses, and said he'd just as much like to be behind a keyboard than playing guitar.

After the release of The Bends, Jonny, went to a doctor because of pain in his arm. His aggressive playing style resulted in him wearing a brace on his arm. It has become a sort of trademark since. He says it doesn't bother him, "it's like taping your fingers before a boxing match".

Jonny's guitars also feature cut-off switches placed to cut the signal from the pickups. The result is a staccato on-then-off note, e.g. the last solo to just and several places in Paranoid Android. The name of the switch goes by the title 'momentary' since it cuts the signal momentarily. To fix the simple way, simply insert the switch across the wire connecting the output jack (where you plug your lead in), and volume knob. There are two wires leading to the output jack, so make sure you connect it to the wire leading to the volume resister and note the tone controls. Jonny places the switch on the metal plate (on a Tele) between the volume and tone dials (can be seen on all his Tele's). If you want to do this, simply drill a hole through the plate, but remember to remove it from your guitar first! Note that Jonny's guitars are rewired, and so he would've probably fitted the switches differently.