I graduated high school in 98, so the 90s is a very special decade of music for me. Alternative, Indie Rock, Grunge, Techno, Industrial, Hardcore and Nu-Metal. Just too much for there to be a best without further specification. Since there isn't much representation on the hind end of that decade I will mention Helmet, Deftones, Vision of Disorder and Earthtone9.
FWIW, my moniker for my hobby pedal building is my favorite Dinosaur Jr song I discovered as a teen off the Reality Bites soundtrack way back then.