Egoyan has subsequently continued making his own idiosyncratic, often satirical brand of brightly-hued and darkly-themed musings on sexuality, politics and the media. While his films generally divide audiences, he has emerged as a thought-provoking filmmaker unafraid to explore seeming taboo subjects. "Speaking Parts" (1989) examined the sexual intersection of and communications between three disparate individuals: a dour woman (Arsinee Khanjian) obsessed with an aspiring actor (Michael McManus) who, in turn, becomes involved with a novice screenwriter (Gabrielle Rose). In 1991's "The Adjuster", Egoyan furthered explored such issues, adding voyeurism and censorship into the mix and laced them with symbolic images and sequences that were striking but not always comprehensible. "Calendar" (1993) was essentially a two-hander, in which the director starred as a photographer who travels to Armenia with his dissatisfied wife (Khanjian). The film explored themes of national identity and heritage, commitment and separation, and the cold effect of a camera lens. While not inaccessible, it was hardly mainstream either. In 1994, Egoyan wrote and directed the intriguing "Exotica", an intricately-plotted, haunting look at human despair. The stories of five individuals become interwoven as they cross paths at the titular strip club. As with many of his works, the themes of observation and desire mixed with his metaphorical and literal use of mirrors.

With "The Sweet Hereafter" (1997), an adaptation of Russell Banks' novel about the aftermath of a tragic schoolbus accident, Egoyan created his most complex work to date. Eschewing the inherent sentiment of the material in favor of a more restrained approach, the writer-director retained some of the more unconventional storytelling aspects of his work, but added a layer of emotional weight lacking in his previous screen outings. As in his other films, "The Sweet Hereafter" raised a number of disturbing (and perhaps unanswerable) questions ranging from how to grieve for loved ones to how to cope with societal changes. As it did not offer pat answers or Hollywood-style happy endings, the film proved compelling and disturbing. Surprisingly Egoyan received two Academy Award nominations for the film, as Best Director and for Best Adapted Screenplay.

In 1997 Egoyan directed a one-hour film featuring renowned cellist Yo-Yo Ma as himself in series of chance encounters with people who had no connection to one another except through his music; the film was shown at Venice International Film Festival. In 1999 the writer-director saw the release of his next major motion picture, the potent psychological thriller "Felicia's Journey" (adapted from William Trevor's novel), which focused on a seemingly kind and genteel caterer (Bob Hoskins) who hides a secret life-even to himself-as a serial killer, and his relationship with 17-year-old, pregnant Felicia, who seems poised to either become his next victim or awaken him to his hideous crimes. Another perfect exercise in masterfully atmospheric direction, the film was a critical and art house favorite and won four Genie Awards, including Best Adapted Screenplay for Egoyan and Best Actor for Hoskins. Egoyan's next major work was 2002's "Ararat," which chronicled the estranged members of a contemporary Armenian family as they faced both Turkey's denial of their catastrophic past and with their own complicated future.

2005 saw the release of Egoyan's next film, the sly and seductive show biz noir "Where the Truth Lies" (2005) starring Kevin Bacon and Colin Firth as a 1950s superstar comedy duo (a la Jerry Lewis and Dean Martin) caught up in the mysterious murder of a beautiful blonde who turns up naked and dead in the bathtub of their New Jersey hotel room, leading to the disolution of their partnership and a years-later investigation. A wonderfully photographed, complexly plotted adult entertainment, the film was Egoyan's most alluring and accessible work to date.