After his stint on "Buffy," Green went on to land several significant film roles. He reprised his role in the Austin Powers sequels of 1999 and 2002 and had parts in "America's Sweethearts" (2001) and "Rat Race" (2001). In 2002, Green starred along with Eugene Levy and Sarah Silverman in the Fox series which featured puppets as talking characters, "Greg the Bunny." While the show only lasted one season, it received favorable reviews and developed a loyal cult following. He then joined John Malkovich, Vin Diesel, Dennis Hopper and Barry Pepper in the minor mobster comedy "Knockaround Guys" (2002); was especially winning in his comedic supporting role in 2003's underrated heist remake "The Italian Job" playing the gadget guru Lyle who claims an idea was stolen from him by a major computer company; his acting skills were also applauded when he played the flamboyant '80s costumed club kid and party promoter James St. James in "Party Monster" (2003).
Green had reached a career point where it was time to try carrying films on his own—or at least with a little help from fellow stars of near-breakout status, teaming in his first bid with Matthew Lillard and "Punk'd" veteran Dax Shephard in the uneven but occasionally amusing backwoods comedy "Without a Paddle" (2004), playing three friends who set out to find bank robber D.B. Cooper's missing stash—Green had one of film's best scenes when his neurotic doctor character goes one-on-one against Bart the Bear. He next appeared in “Scooby-Doo 2: Monsters Unleashed” (2004), playing a museum curator who’s suspected of being an anonymous masked villain wreaking havoc on the city of Coolsville by unleashing supernatural foes created by his monster machine. Green next created and voiced characters in the Cartoon Network’s satirical “Robot Chicken” (2004- ), a stop-motion animated series that parodied pop culture by using toys, dolls and claymation—everything from Transformers to Michael Jackson to Final Fantasy VII were skewered by Green and co-creator, Michael Senreich. Meanwhile, Green had a run on the live-action sitcom, “Four Kings” (NBC, 2005-2006), a series that focused on four New Yorkers who have been friends since childhood.