For eleven years Murphy was a writer for MST3K; for nine of those years, he also voiced and operated the robot Tom Servo, replacing original cast member J. Elvis Weinstein. After taking over the role of Servo, an anonymous person sent him a banner that read "I Hate Tom Servo's New Voice". Flattered by the enormous amount of effort taken to heckle him, Murphy hung the banner in his office for over a year. During the final three years of the series, he additionally portrayed Professor Bobo, an English-speaking mountain gorilla in the style of Planet of the Apes. After the end of MST3K, Murphy spent the year 2001 going to a different movie every day and wrote a book about this experience, entitled . During his year at the movies, Murphy samples theatres from small-town boxes to urban megaplexes, attempts a theatre-food diet, suffers a kidney stone, visits both the Sundance and Cannes film festivals, sneaks Thanksgiving dinner into a showing of Monsters, Inc., and records all of these experiences, both good and bad. His feat – viewing over four hundred films on four continents – was mentioned in Ripley's Believe It or Not.
RiffTrax era
Since 2006, Murphy has joined Michael J. Nelson on many audio commentaries for Nelson's RiffTrax movie-riffing website, along with MST3K alumnus Bill Corbett. He was notably absent from Joel Hodgson's Cinematic Titanic series, which included most of the original cast of Mystery Science Theater 3000. During a 2008 interview, Hodgson was asked if Murphy harbored any sort of animosity towards him or the Cinematic Titanic members; he responded: "I can't really speak for him. We saw him at ComicCon, and we did the Mystery Science Theater 20th anniversary panel, and he seemed totally happy to be there, willing to be there, but he's doing RiffTrax." Murphy also did not appear in a 2008 reunion sketch, which otherwise featured all of the original cast members from the Comedy Central era reprising their roles. The brief skit was included as a bonus feature on The Giant Gila Monster disc of the MST3K Volume 10.2 DVD. In 2013, Murphy recorded a voice for the computer gameTesla Effect, playing Smart Alex, a Siri-like AI assistant that heckles the player's failures. Murphy resides in the Minneapolis-St. Paul area with his wife, Jane.