Following small roles in Dennis Hopper's "Backtrack" (1990) and Blake Edwards' "Switch" (1991), Keener received her big break as the level-headed and loving Yvonne, confronting Brad Pitt's preening would-be pop star in cinematographer Tom DiCillo's writing-directing debut "Johnny Suede" (also 1991), which inaugurated her longstanding collaboration with the director. Feeling she had not got near her due for that picture, DiCillo wrote a part with her in mind, filming first the self-contained short "Scene Six, Take One" (1994) before expanding it into the feature "Living in Oblivion" (1995). An insider's look at low-budget filmmaking, it featured a wicked send-up of Pitt in the guise of James Le Gros, playing an egocentric, blond-maned star wreaking havoc on a shoestring shoot. Keener starred as an actress who, together with the inept director (Steve Buscemi), cinematographer (Mulroney) and crew, precipitates endless takes of a particularly emotional scene, and DiCillo took his shots at Pitt, showing how an all-powerful star can throw his weight around both overtly and covertly.

Keener was the girlfriend of a boxer-turned-hitman (Alan Gelfant) in "The Destiny of Marty Fine" (1995) and had a small role in Stacy Cochran's "Boys" (1996) before Nicole Holofcener's gal-pal film "Walking and Talking" (also 1996) gave her a strong role as a continual loser in love who must come to terms with the impending marriage of her best friend (Anne Heche). That same year, the busy actress portrayed Demi Moore's judgmental sister-in-law in the Nancy Savoca scripted and helmed segment ("1952") of HBO's "If These Walls Could Talk" (in which Heche also appeared in the Cher-directed "1996") and reunited with DiCillo for the small-town comedy "Box of Moonlight", playing a flaky local who romances John Turturro. The following year found her back with DiCillo for "The Real Blonde", his comic exploration of the quest for integrity in the superficial worlds of fashion advertising, rock videos and soap operas. Her job as a makeup stylist for a hotshot fashion photographer (Marlo Thomas) paid most of the bills accrued in her relationship with aspiring actor (no agent, no credits) Matthew Modine, who kept trying to resist the charms of Elizabeth Berkeley.

Keener upped her mainstream profile with a cameo as George Clooney's former mistress in "Out of Sight" (1998), adapted from Elmore Leonard's novel, and by portraying Nicholas Cage's faithful wife in "8mm" (1999). In between she appeared in the ensemble of Neil LaBute's "Your Friends & Neighbors" (also 1998), a biting look at the tangled relationships of a group of bright, endlessly loquacious urbanites. As Ben Stiller's significant other, Keener impressed as a woman who realizes her relationship (particularly its sexual component) is not working and determines to do something about it by engaging in a lesbian affair. Enjoying a bit of role reversal in Spike Jonze's "Being John Malkovich" (also 1999), she earned a Best Supporting Actress Oscar nomination as the sexy, bitchy Maxine who finds herself in a love triangle involving a puppeteer (John Cusack) and his wife (a surprisingly frumpy Cameron Diaz), the three of them absolutely gaga about being able to spend time inside Malkovich's head. She then finished another productive year as Nick Nolte's abandoned girlfriend whom Jeff Bridges involves in the resolution of a decades old con in "Simpatico", Matthew Warchus' screen adaptation of Sam Shepard's play. In 2002, Keener was one of the high points in Steven Soderbergh's disappointing return-to-indie-style feature "Full Frontal," yet again creating a character with a potent combination of compelling and unsympathetic qualities. Worse for the actress was Danny DeVito's dull and unfunny "Death to Smoochy" (2002), in which she played a TV executive caught in a war between two TV kiddie show hosts (Edward Norton and Robin Williams), and her ease at playing career women with tough exteriors veered into typecasting territory when she appeared in "S1m0ne" (2003), the tale of the success of a computer-generated actress.

Keener earned raves for her role in writer-director Rebecca Miller's low-profile indie "The Ballad of Jack & Rose" (2005) as the girlfriend of a protective father (Daniel Day-Lewis) whose integration into the family threatens his young daughter (Camilla Bell). She then had a welcome supporting turn in the thriller "The Interpreter" (2005), playing the wisecracking partner of Sean Penn's federal agent, before being cast in one of her most appealing roles yet as Trish, the alluring, good-natured, too-young grandmother who become the object of the sexually inexperienced Steve Carell's affection in the hit comedy "The 40 Year-Old Virgin" (2005). Keener infused the character with a genuine warmth and middle-aged sexiness that led audiences to invest in the relationship and helped the film add a more sweet and involving element to its otherwise R-rated arsenal of sex-related jokes. She then played the pivotal role of Nelle Harper Lee in “Capote” (2005), the soon-to-be Pulitzer Prize winner of “To Kill A Mockingbird” fame who helped friend and author Truman Capote (Philip Seymour Hoffman) investigate a grisly quadruple murder in Holcomb, Kansas that became the eccentric writer’s true crime classic, In Cold Blood. Keener was nominated for several awards, including an Academy Award for Best Actress in a Supporting Role.