Casting
Following Parisot's assignment as director, Allen was quickly cast as Nesmith, and had to choose between Galaxy Quest and Bicentennial Man. The Bicentennial Man role went to Robin Williams. Allen said he was a big sci-fi fan and had hoped the role would launch a second part of his career as a sci-fi actor. Some of Allen's sci-fi knowledge was put to use during production: for example, when the crew is about to land on an alien planet, Allen brought up the issue of a breathable atmosphere with Johnson and Parisot; this became dialogue for Fleegman and Kwan in the movie. About his role, Allen said he based his performance more on Yul Brynner's Ramesses II from the 1956 The Ten Commandments, and less on William Shatner as Captain James Kirk from Star Trek.
Alan Rickman was selected to be Alexander Dane, who played the alien Dr. Lazarus. Rickman had been interested in the part not so much for the sci-fi elements, but because of the humor. He said "I love comedy almost more than anything. This really is one of the funniest scripts I've read," and that "actors are probably the only professionals who send themselves up. We actually have a sense of humor about ourselves." While the original script made Dane a ceremonial knight, Rickman suggested the title would be too much for the character, and this was dropped, though he remained listed as "Sir Alex Dane" in the credits. Rickman also provided input into the prosthetic piece that Dane would use to play Lazarus, saying "it was important for it to be good enough to convince the aliens who believe we're the real thing, but also cheesy enough to imagine that it was something he applied himself". Rickman's sense of drama came into play during initial reads and script revisions. Rockwell said that Rickman "was very instrumental in making sure the script hit the dramatic notes, and everything had a strong logic and reason behind it". The scene where Dane, as Dr. Lazarus, gives a final, powerfully emotional speech to Quellek, played by Patrick Breen, used Rickman's sense of drama, according to Rockwell. Dr. Lazarus' catchphrase, "By Grabthar's Hammer", was written as a temp line in Gordon's script; Gordon planned to replace "Grabthar" with something less comical, but the line stuck as the production crew started using it around their offices and had it printed on t-shirts.
Weaver had loved the script since her first read when Ramis was the director, stating "that great sort of Wizard of Oz story of these people feeling so incomplete in the beginning, and then during the course of this adventure, they come out almost like the heroes they pretended to be in the first place." She particularly loved the part of Madison: "to me she was what a lot of women feel like, including myself, in a Hollywood situation." In addition, she had long wanted to work with both Allen and Rickman. Once Parisot replaced Ramis, Weaver lobbied Parisot to cast her, insisting that Madison needed to be blonde and have large breasts to capture the humor of a sci-fi production. She was surprised when she got the role. Weaver said that this role, given some of her personal insecurities, was closer to "telling the truth about myself and science fiction" compared to her performance as Ripley in the Alien films. She wore a blonde wig (which she kept after production) and an enhanced bosom, which many of the crew said gave Weaver a new personality. Weaver often left the set in costume and returned to her hotel to admire herself, saying that she "loved being a starlet."
Tony Shalhoub originally auditioned for Guy Fleegman until Sam Rockwell was cast. Shalhoub was cast as Fred Kwan and worked with Parisot to develop the character. Kwan was loosely based on David Carradine, who was a non-Asian in an Asian role in the television series Kung Fu. Additionally, it was rumored that Carradine frequently acted while under the influence of drugs. Although Shalhoub could not overtly portray a "stoner" in a PG-13 film, he insisted that Kwan should always be shown eating to subtly reference the stoner stereotype.
Rockwell, who wanted to develop a more serious dramatic acting career, initially considered declining the role after he was cast. He eventually recognized that several successful dramatic actors had done comedy roles early on, and fellow actor Kevin Spacey persuaded him to take the part. He was the last of the main actors to be cast. Rockwell fashioned Fleegman after cowardly characters from other films, such as John Turturro's Bernie in Miller's Crossing, Bill Paxton's Private Hudson in Aliens, and Michael Keaton's "Blaze" in Night Shift. Rockwell drank a lot of coffee before certain scenes to help create the over-excitement and jitters associated with the character. Rockwell's character's name, Guy Fleegman, is a homage to Guy Vardaman, a little-known actor who worked extensively on Star Trek either as a stand-in or in bit roles. Rockwell and Shalhoub improvised some dialog to contrast Fleegman as an alarmist while Kwan was always nonchalant. Daryl Mitchell had worked with Parisot on Home Fries, and Parisot felt he was the perfect choice to play Webber. David Alan Grier was "head to head" with Mitchell for the part, according to Mitchell.
Justin Long was cast as Brandon, and it was Long's first feature-film role. Long had just completed a pilot for a television show under casting director Bonnie Zane, who suggested Long to her sister Debra Zane, the casting director for Galaxy Quest. Long said he was nervous auditioning as an unknown actor at the time, competing against Kieran Culkin, Eddie Kaye Thomas, and Tom Everett Scott. Parisot had given Long a copy of Trekkies, a film about the Star Trek fandom, to help prepare for the character. Long based his character on a combination of Philip Seymour Hoffman's Scotty J. from Boogie Nights and the Comic Book Guy from The Simpsons. Paul Rudd auditioned for a role.
One of the first "Thermians" to audition was Enrico Colantoni. Colantoni loved the script and spent time before his audition developing the behavior he thought the Thermians should have. Parisot said that at the end of Colantoni's read, the actor offered a possible voice for the Thermians. Parisot immediately loved the voice and used it to establish the nature of the Thermians for the rest of the casting process. Colantoni led how the Thermians would act, which he called "happy Jehovah's Witnesses" taking everything in with "love and acceptance." Other actors cast as Thermians included Jed Rees and Rainn Wilson (his feature-film debut). According to Debra Zane, they had "a difficult time finding an actress to play a Thermian. Ultimately, Zane was so impressed with Missi Pyle's audition that she sent the casting tape directly to Parisot, with a note stating "If this is not Laliari, I will resign from the CSA." Steven Spielberg, also impressed by Pyle and on set for a day, suggested Laliari's role to be expanded, which developed into the romance with Kwan. Jennifer Coolidge also auditioned for the role.
Actors cast as Thermians went to "alien school" to learn how to move and talk, since they were "basically giant calamari hiding in human shape", according to Parisot. The walk was inspired by how the marionettes were articulated in the series Fireball XL5. Other idiosyncrasies were developed by the actors during this training, and several of their lines came out of improvisations. Wilson's role as Lahnk was to have been larger in the film, but the actor was double-booked for an NBC pilot in New York City. He received a crash course on how to act like a Thermian from Colantoni, Rees, and Pyle, but still was nervous around the A-list actors leading the cast. Wilson said that a deleted scene involving Lahnk, released with the film's home media, was wisely cut given how nervous he was, flubbing his lines several times.