Following Happy Endings, she had five film releases in 2006: Trust the Man, Stranger than Fiction, Monster House, World Trade Center, and Sherrybaby.
In Trust the Man, featuring Julianne Moore, David Duchovny, and Billy Crudup, she played Elaine, who has been dating Tobey, Crudup's character, for seven years and has begun to feel that it is time for her to settle down and start a family.
The film was critically and financially unsuccessful.
Ethan Alter of Premiere felt that the performances by Gyllenhaal and Duchovny were "much more at ease" and concluded with "that's probably because they're  [sic] played these characters many times before".
In Stranger than Fiction, Gyllenhaal played a love interest of Harold Crick, played by Will Ferrell.
Her performance in the film received favorable reviews; Mike Straka of Fox News wrote: "Gyllenhaal has never been sexier in any film before and her interplay with Ferrell will propel her to more A-list films, leaving her indie-darling days behind, no doubt."
She voiced Elizabeth "Zee" in the computer animated horror film Monster House.
Gyllenhaal played Allison Jimeno, the wife of Port Authority officer Will Jimeno, in Oliver Stone's World Trade Center, based on the September 11 attacks in New York City.
She regarded this as "one of the films she most enjoyed making".
The film received favorable reviews and proved to be an international success, earning US$162 million worldwide.

In Sherrybaby, Gyllenhaal played a young drug-addicted thief trying to put her life in order after prison so she can reconcile with her daughter.
During promotion of the film, she noted of her portrayal of the character: "I think she's in such dire straits that all she has are these kind of naive, fierce hopes.
And while I was playing the part I was looking for pleasure and hope in everything, even in these really bleak things.
And so it was really mostly after I finished the movie that I felt pain."
Her performance in the film was well-received; David Germain of the Associated Press wrote, "Gyllenhaal humanizes her so deeply and richly ... that Sherry elicits sympathy even in her darkest and weakest moments", and Dennis Harvey of Variety called her performance "naturalistic".
For her performance, Gyllenhaal earned a second Golden Globe Best Actress nomination and won the Best Actress category award at the 2006 Stockholm International Film Festival.

She appeared in The Dark Knight (2008), the sequel to Batman Begins (2005), in which she replaced Katie Holmes as Assistant District Attorney, Rachel Dawes.
Gyllenhaal acknowledged her character was a damsel in distress to an extent, but said director Christopher Nolan sought ways to empower her character, so "Rachel's really clear about what's important to her and unwilling to compromise her morals, which made a nice change" from the many conflicted characters she had previously portrayed.
The Dark Knight was a critical and commercial success, setting a new opening weekend box office record for North America.
With revenue of $1 billion worldwide, it became the fourth-highest-grossing film of all time, and remains Gyllenhaal's most commercially successful feature to date.
In a Salon review of the film, Stephanie Zacharek called Gyllenhaal's character "a tough cookie in a Stanwyck-style bias-cut dress" and stated that "the movie feels smarter and more supple when she's on-screen".
IGN film critic Todd Gilchrist wrote, "Gyllenhaal adds real depth and energy to Rachel Dawes".

In addition to film, Gyllenhaal played Yelena Andreevna in the Classic Stage Company's 2009 Off-Broadway production of Anton Chekhov's Uncle Vanya in New York City.
The cast also included her husband Peter Sarsgaard.
The production, directed by Austin Pendleton, began previews on January 17 and ended its limited run on March 1.
Joe Dziemianowicz of the New York Daily News was unenthusiastic about her performance, writing "Gyllenhaal, who was so dynamic as a druggie in the film Sherrybaby, plays Yelena with a slow-mo saunter and monotonous pasted-on smile that makes it seem as if she's been in Sh
Following Happy Endings, she had five film releases in 2006: Trust the Man, Stranger than Fiction, Monster House, World Trade Center, and Sherrybaby. In Trust the Man, featuring Julianne Moore, David Duchovny, and Billy Crudup, she played Elaine, who has been dating Tobey, Crudup's character, for seven years and has begun to feel that it is time for her to settle down and start a family. The film was critically and financially unsuccessful. Ethan Alter of Premiere felt that the performances by Gyllenhaal and Duchovny were "much more at ease" and concluded with "that's probably because they're  [sic] played these characters many times before". In Stranger than Fiction, Gyllenhaal played a love interest of Harold Crick, played by Will Ferrell. Her performance in the film received favorable reviews; Mike Straka of Fox News wrote: "Gyllenhaal has never been sexier in any film before and her interplay with Ferrell will propel her to more A-list films, leaving her indie-darling days behind, no doubt." She voiced Elizabeth "Zee" in the computer animated horror film Monster House. Gyllenhaal played Allison Jimeno, the wife of Port Authority officer Will Jimeno, in Oliver Stone's World Trade Center, based on the September 11 attacks in New York City. She regarded this as "one of the films she most enjoyed making". The film received favorable reviews and proved to be an international success, earning US$162 million worldwide.
In Sherrybaby, Gyllenhaal played a young drug-addicted thief trying to put her life in order after prison so she can reconcile with her daughter. During promotion of the film, she noted of her portrayal of the character: "I think she's in such dire straits that all she has are these kind of naive, fierce hopes. And while I was playing the part I was looking for pleasure and hope in everything, even in these really bleak things. And so it was really mostly after I finished the movie that I felt pain." Her performance in the film was well-received; David Germain of the Associated Press wrote, "Gyllenhaal humanizes her so deeply and richly ... that Sherry elicits sympathy even in her darkest and weakest moments", and Dennis Harvey of Variety called her performance "naturalistic". For her performance, Gyllenhaal earned a second Golden Globe Best Actress nomination and won the Best Actress category award at the 2006 Stockholm International Film Festival.
She appeared in The Dark Knight (2008), the sequel to Batman Begins (2005), in which she replaced Katie Holmes as Assistant District Attorney, Rachel Dawes. Gyllenhaal acknowledged her character was a damsel in distress to an extent, but said director Christopher Nolan sought ways to empower her character, so "Rachel's really clear about what's important to her and unwilling to compromise her morals, which made a nice change" from the many conflicted characters she had previously portrayed. The Dark Knight was a critical and commercial success, setting a new opening weekend box office record for North America. With revenue of $1 billion worldwide, it became the fourth-highest-grossing film of all time, and remains Gyllenhaal's most commercially successful feature to date. In a Salon review of the film, Stephanie Zacharek called Gyllenhaal's character "a tough cookie in a Stanwyck-style bias-cut dress" and stated that "the movie feels smarter and more supple when she's on-screen". IGN film critic Todd Gilchrist wrote, "Gyllenhaal adds real depth and energy to Rachel Dawes".
In addition to film, Gyllenhaal played Yelena Andreevna in the Classic Stage Company's 2009 Off-Broadway production of Anton Chekhov's Uncle Vanya in New York City. The cast also included her husband Peter Sarsgaard. The production, directed by Austin Pendleton, began previews on January 17 and ended its limited run on March 1. Joe Dziemianowicz of the New York Daily News was unenthusiastic about her performance, writing "Gyllenhaal, who was so dynamic as a druggie in the film Sherrybaby, plays Yelena with a slow-mo saunter and monotonous pasted-on smile that makes it seem as if she's been in Sh
Maggie Gyllenhaal