i always really liked Mike Ness' playing and tone. Its very basic: les paul -> boss sd1 -> bassman but it has a timeless quality that wasn't as common in the 90s where people got obsessed with more noisy and less vocal lead sounds. Kinda like how in the 80s Slash plugged a les paul into a marshall and made simple sounds cool again and have everyone selling their racks.
on the opposite side of that you gotta throw some props to Adam Jones. His rig was also fairly basic, but his sound was very unique with Tool. Lots of noise, lots of color. Not exactly vocal, but aggressive and also atmospheric and moody. Most guys aren't going to sound like that with essentially a very similar rig to what Slash and his clones were playing in the 80s.
I was about to type Marc Ribot on Rain Dogs. But Rain Dogs was released in 1985. But this was released in 1998, so Marc Ribot is the guy who I think had the most unique tone I can think of from the 1990s.
But Sir Richard Bishop had an interesting tone too on this record from 1993.
I think Billy Corgan stands out as the guitar God of that era. His tone from that period is instantly recognizable. Don't think anyone has taken multitrack guitar laying to quite an extreme before or after either...