Almost every name in Jojo's Bizarre Adventure can be traced to being some sort of musical reference. It'd probably be faster to list the names that aren't direct references!
In order to even attempt to answer the question accurately, it's necessary to define what constitutes being "from the 90's". Must the song or artist have debuted in the 1990s? Is it enough for the artist to have been active during the 90s even if they started earlier? Would a 1990s re-release of a song or album that debuted earlier count?
For the record, chapter 151 of the manga (one-fourth of the way through Part 3, Stardust Crusaders) debuted on January 1, 1990, while chapter 595 (the start of Part 6, Stone Ocean) debuted on January 1, 2000. So the entirety of Part 4 (Diamond is Unbreakable) and Part 5 (Vento Aureo) was written during the 1990s. However, this doesn't guarantee that every musical reference made during that time is topical. For example, Part 5's White Album references a Beatles release from 1968, while Part 4's Super Fly references a film and soundtrack from 1972.
As for which 90s song besides "I Want You" is used for the anime ending sequences, the first ending theme for Golden Wind is "Freek'n You" by Jodeci.