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1990–2004: Continued work

Allen's 1991 film Shadows and Fog is a black-and-white homage to the German expressionists and features the music of Kurt Weill. Allen then made his critically acclaimed comedy-drama Husbands and Wives (1992), which received two Oscar nominations: Best Supporting Actress for Judy Davis and Best Original Screenplay for Allen. Manhattan Murder Mystery (1993) combined suspense with dark comedy and marked the return of Diane Keaton, Alan Alda and Anjelica Huston.

He returned to lighter fare such as the showbiz comedy involving mobsters Bullets Over Broadway (1994), which earned an Academy Award nomination for Best Director, followed by a musical, Everyone Says I Love You (1996). The singing and dancing scenes in Everyone Says I Love You are similar to musicals starring Fred Astaire and Ginger Rogers. The comedy Mighty Aphrodite (1995), in which Greek drama plays a large role, won an Academy Award for Best Supporting Actress for Mira Sorvino. Allen's 1999 jazz-based comedy-drama Sweet and Lowdown was nominated for two Academy Awards, for Sean Penn (Best Actor) and Samantha Morton (Best Supporting Actress). In contrast to these lighter movies, Allen veered into darker satire toward the end of the decade with Deconstructing Harry (1997) and Celebrity (1998).

On March 8, 1995, Allen's one-act play Central Park West opened off-Broadway as a part of a larger piece titled Death Defying Acts, with two other one-act plays, one by David Mamet and one by Elaine May. Critics described Allen's contribution as "the longest and most substantial of the evening". During this decade Allen also starred in the television film The Sunshine Boys (1995), based on the Neil Simon play of the same name, and made a sitcom "appearance" via telephone in a 1997 episode, "My Dinner with Woody", of Just Shoot Me! that paid tribute to several of his films. He provided the voice of Z in DreamWorks ' first animated film, Antz (1998), which featured many actors he had worked with; Allen's character was similar to his earlier roles.

Small Time Crooks (2000) was Allen's first film with the DreamWorks studio and represented a change in direction: he began giving more interviews and made an attempt to return to his slapstick roots. The film is similar to the 1942 film Larceny, Inc. (from a play by S. J. Perelman). Allen never commented on whether this was deliberate or if his film was in any way inspired by it. Small Time Crooks was a relative financial success, grossing over $17 million domestically, but Allen's next four films foundered at the box office, including Allen's most costly film, The Curse of the Jade Scorpion (with a budget of $26 million). Hollywood Ending, Anything Else, and Melinda and Melinda have "rotten" ratings on film-review website Rotten Tomatoes and each earned less than $4 million domestically. Some critics claimed that Allen's early 2000s films were subpar and expressed concern that his best years were behind him. Others were less harsh; reviewing the little-liked Melinda and Melinda, Roger Ebert wrote, "I cannot escape the suspicion that if Woody had never made a previous film, if each new one was Woody's Sundance debut, it would get a better reception. His reputation is not a dead shark but an albatross, which with admirable economy Allen has arranged for the critics to carry around their own necks."