I've recently read an interview with Jason Newsted. It was from 96, when they were doing the Load-Tour. There he explains, how he achieves his sound in the studio. The interview has been translated into german, so I will try to translate it, rather than give you the link. He says that he usually used a '82 Spector Bass and a '58 Fender Precision (also on the black album). For 'Until It Sleeps' he used a Zon fretless bass. Amp-wise he especially used SVT Tops, his main one was from the 70's. For the Load-album he also used Mesa/Boogie amps with 15" and 18" cabinets and an old 400 watts Fender with an 18" folded cab. In the studio, they used 3-4 different rooms for the amps. One for the Ampeg and Mesa/Boogie cabs, which were miked with ten (!) mics. Then they had another room for the Fender, that was used for the ultra-low frequencies. In addition, he used old Gibson amps and the Mini-Marshall Stack for the distortion sound. They miked that damned little thing with three microphones! The effects he used were MXR Flangers and Phasers, a SansAmp and a Tech 21 XXL distortion pedal. For noise effects, he used Mutrons. And finally, in addition to all that, they took a DI signal through an tube-DI box.