Amps
Jones owns and uses a vintage Marshall head, which is a non-master volume bass amplifier from 1976, Mesa Boogie dual rectifier (original, 2 channel version) and a Diezel VH4 amplifier. On Undertow and the Opiate EP the Marshall bass amplifier was used, as the mesa boogie dual rectifier and the Diezel were not around in 1993 or before. On Ænima the Marshall amplifier was used for high frequencies [treble]. The Diezel VH4 was used to contribute the bass and mid range frequencies. The two amps were mixed accordingly to level out the frequencies. Lateralus was recorded with the Diezel amp, along with the Marshall bass amp. Occasionally, a SUNN head was used instead of the Mesa Boogie rectifier in the studio, but the Mesa Boogie is still used on stage.
When playing live, Adam Jones' amps are all on at the same time, and are all on a "dirty" setting (distortion or commonly referred to as gain). To switch to a "clean" tone (undistorted) he simply rolls the volume on his guitar back enough to get a semi clean tone, and then plays the notes very gently without much attack on the strings from the pick to achieve a somewhat clean tone.
Effects
Adam Jones uses an Ibanez digital delay pedal but has also been known to use the Line 6 DL-4 delay pedal. Additionally, he uses an Ibanez flanger and a Crybaby wah 535Q model for some lead breaks. The boss graphic EQ pedal he uses, is always left on. It has the mid-range frequencies on full for a rhythm sound that is associated with Tool.
Jones also uses an "Epilady", a razor-like item used to rip off leg hair. In an interview, he explained that he took one apart and found that they have a spinning wire similar to that of a guitar string. He uses it by striking it gently on the strings. Jones also has a "Leslie" simulator which can be heard on "Die Eier Von Satan" off Ænima.