Missy Elliott, Eminem, Evanescence, 50 Cent, Chad Hugo, Ricky Skaggs, Justin Timberlake, Luther Vandross and the late Warren Zevon had five nominations each.
Nominations for the 46th annual Grammy Awards were announced at a Beverly Hilton press conference.
Among the nominations for Hugo and Williams were three for their work with The Neptunes.
Beyonce and her beau, rapper Jay-Z, were among contenders for record of the year for "Crazy in Love," along with the Blackeyed Peas' and Justin Timberlake's "Where is the Love?" Other nominees were Coldplay's "Clocks," Eminem's "Lose Yourself" and OutKast's "Hey Ya."
Album of the year contenders were Elliott's "Under Construction," "Fallen" by Evanescence, "Speakerboxxx/The Love Below" by OutKast, "Justified" by Timberlake and "Elephant" by The White Stripes.
The dark rock group was also represented in the best new artist category alongside thug rapper 50 Cent, the alt-pop group Fountains of Wayne, R&B singer Heather Headley and dance hall DJ Sean Paul.
The song of the year nominations, which go to songwriters, went to Linda Perry for Christina Aguilera's "Beautiful," Richard Marx and Vandross for Vandross' "Dance With My Father" and Avril Lavigne and the songwriting group The Matrix for Lavigne's "I'm With You."
Others were Jorge Calderon and Zevon for the later entertainer's reflection on mortality "Keep Me in Your Heart." Zevon died from lung cancer at age 56 on Sept. 7. The songwriter nominees were Jeff Bass, Eminem and Luis Resto for Eminem's "Lose Yourself."