Graham had a small part in the acclaimed "Mrs. Parker and the Vicious Circle" (also 1994), and took the starring role in the direct-to-video release "Toughguy/Terrified" (1995), before offering a memorable supporting turn as Lorraine, a swing dancing beauty who is able to pull Jon Favreau's heartbroken Mike out of his funk in 1996's "Swingers". This role helped to re-establish Graham, who was next seen in 1997's celebrated "Boogie Nights" as Rollergirl, a young porn star who is never without her skates. Graham's energetic portrayal of Rollergirl, the 'daughter' of the film's surrogate family setup, conveyed a surprising and touching innocence and humor, with her uncharacteristic brutal attack on a high school tormentor near the film's end serving as a particularly well-acted dramatic highlight. She followed this attention-grabbing performance with a cameo in "Scream 2", playing Drew Barrymore's character from the original in "Stab", the slasher film-within-a-slasher film. Also in 1997, Graham co-starred with Natasha Gregson Wagner and Robert Downey Jr. in "Two Girls and a Guy", a real-time look at a wandering boyfriend, and the confrontation between him and two of his misled lovers. She was a shining part of the otherwise disappointing film, and the eye-flashing ferocity unleashed in her scenes with Downey proved her more than just a pretty face.

After the overt sexuality of her last two starring efforts, Graham went studious as Dr. Judy Robinson in the feature adaptation of "Lost in Space" (1998), spurning the advances of Matt LeBlanc and outfitted from wrist to ankle in modest astro-jumpsuits. In 1999 she reached her largest audience, co-starring as Felicity Shagwell, 1960s CIA agent in the blockbuster sequel "Austin Powers: The Spy Who Shagged Me". Decked out in risqué mod-meets-flower child gear and purring memorably cheeky lines such as "Shagwell by name, shag very well by reputation", Graham's sweet and sultry presence was the perfect swinging counterpart to Mike Myers' Powers. She followed up with a role in the comedy "Bowfinger" (also 1999), starring alongside Steve Martin (who also penned the script) and Eddie Murphy as a young Hollywood hopeful, fresh from Ohio who dates her way to the top, only to break the heart of her last conquest (Martin) when she leaves him to cash in on the precarious lesbian chic with a powerful Tinseltown woman. Her character's similarity to Graham's previous co-star (and Martin's former love interest) Anne Heche sparked much speculation. In 2000, Graham starred opposite Luke Wilson as an abandoned wife on a mission to keep her vows, seeking out her husband on a whirlwind road trip in "Committed", a film featuring a cast with dozens of young up and coming actors and hip musicians.

Graham proved to be solid in 2001, starring in the indie romantic comedy "Sidewalks of New York" opposite Ed Burns. Also in 2001, perhaps unwisely, Graham jumped on the teen gross-out train with the gigantic flop "Say It Isn't So." While the movie was produced by the legendary Farrelly brothers, it lacked any kind of a comic spark and was one of a few disasters signaling the end of the repulsive comedy genre. Graham's reputation, however, remained intact after this small misstep, and she was cast as Whitechapel prostitute Mary Kelly in the Hughes brothers' film adaptation of the Jack the Ripper comic book "From Hell" (2001) opposite Johnny Deep. The actress equated herself well, although saddled with a faux British accent and improbably ravishing for a destitute whore in 1880s London.

She next starred in the middling erotic thriller "Killing Me Softly" (2002)opposite Joseph Fiennes, baring much of her body as a woman involved in a kinky affair with a mysterious man; and co-starred in the Indian-themed romantic comedy "The Guru" (2003), with up-and-coming actor Jimi Mistry, where she was cast again as a porn star—although this role was much lighter in tone. She then played a nice, normal girl caught in a romantic triangle between Colin Firth and Minnie Driver in "Hope Springs" (2003) and played a bar patron with a surprising private side caught up in the battle of wills between Jack Nicholson and Adam Sandler in an uncredited turn in "Anger Management" (2003). Graham next starred in the Bollywood-esque romantic comedy, “The Guru” (2003), playing an adult film star whose affections are sought by an Indian dance teacher (Jimi Mistry) seeking his fame and fortune in America.

Graham was able to reheat her career when she signed for an eight episode stint on NBC's cult hit sit-com "Scrubs" in 2004. Appearing as the charmingly off-kilter, fast-talking psychologist Molly Clock, she reminded viewers of her comedic abilities and willingness to whatever it takes to sell a joke. After appearing in an episode of the perpetually uncertain “Arrested Development” (Fox, 2003-2006), Graham landed her own sitcom, “Emily’s Reasons Why Not” (ABC, 2005-2006), playing a book publisher with a string of disastrous relationships who develops a technique to determine suitable men, but is incapable of following her own advice. The network promoted the series relentlessly, running television commercials and hoisting billboard ads as if it were the only show on their slate. The show, however, was canceled its the first episode because of poor ratings. Adding embarrassment to failure, Graham was featured in a cover story of Life magazine calling her “TV’s sexiest star” and touting her new show just days after the cancellation announcement—too late to change once the magazine had already gone to print.