That's the Way I Feel Now: A Tribute to Thelonious Monk, a showcase for acts ranging from Dr. John to Joe Jackson to John Zorn, followed in 1984, and a year later, Willner launched Lost in the Stars: The Music of Kurt Weill, which featured contributions from Sting, Tom Waits, and Lou Reed. After turning to film with work on a pair of 1987 projects, Heaven and Candy Mountain, a year later Willner earned considerable notice for Stay Awake, a tribute to the classic music of Walt Disney's animated films which featured Ringo Starr, Sun Ra, and Sinéad O'Connor. Animated music remained one of his preoccupations in the years to follow, and in 1990 he assembled The Carl Stalling Project, a collection of vintage cartoon scores from the legendary Warner Bros. studio composer. (A sequel appeared in 1995.)

In 1989, Willner began a stint as producer on the innovative but short-lived syndicated television series Michelob Presents, Night Music, followed in 1992 by Weird Nightmare: Meditations on Mingus, another all-star tribute, this time featuring Elvis Costello, Keith Richards, and Henry Rollins. A year later, he collaborated with filmmaker Robert Altman on the acclaimed Short Cuts, a working relationship which extended into 1996's Kansas City and its accompanying Robert Altman's Jazz '34. After wrapping up 1998's Closed on Account of Rabies: Poems and Tales of Edgar Allan Poe (spotlighting performances by Iggy Pop, Ken Nordine, and Jeff Buckley), Willner signed to Howie B.'s Pussyfoot label to release his proper solo debut, Whoops, I'm an Indian!