(written from a Production point of view)
The following are Star Trek parodies and references in prose-based literature.
3001: The Final Odyssey Edit
In the fourth (and final) part of Arthur C. Clarke's Space Odyssey saga, Dr. Frank Poole (played by Gary Lockwood in the film version of 2001: A Space Odyssey) is revealed to be a Star Trek fan, having asked autographs from Leonard Nimoy and Patrick Stewart as a teenager. When choosing 20th century television programs for him, 31st century scientists selected episodes from "all the four Star Trek series" (the novel was published in 1997, long before the debut of Star Trek: Enterprise).
The 4400 Edit
In The 4400 tie-in novel Wet Work by frequent Star Trek authors Dayton Ward and Kevin Dilmore, a character notes he is a fan of pulp-science fiction magazines like Incredible Tales of Scientific Wonder.
Angels & Demons Edit
In Dan Brown's predecessor to The Da Vinci Code, Robert Langdon comments that he has "sort of" heard of antimatter, to which Vitoria Vetra responds, "you watch Star Trek?" Langdon agrees and asks "isn't antimatter what powers the starship Enterprise?" Langdon later holds back from asking about "Captain Kirk using Photon torpedoes against the Klingons."
The sci-fi children's book series Animorphs features many references from Star Trek, like a character called the Ellimist, who is based off Q and the novel Flatland, an alien race called the Hawjabrans, who have freighters that look a little like the USS Enterprise-D, and the females of an alien race called the Ongachic, who look like Worf. Additionally, several of the characters in the series are fans of Star Trek and make comparative references, such as Dracon beams being comparable to phasers and the Andalite law of "Seerow's Kindness" as being a version of the Prime Directive.
A Thing of Beauty Edit
(Written by Lisa Samson) The father of main character Fiona Hume is mentioned to have starred in a sci-fi parody movie called Galaxy Goons in which he played a character named "Captain Quirk". 
The Beach Edit
An early chapter is called "It's life Jim, but not as we know it" (from the well-known parody song "Star Trekkin'"). It involves the narrator playing pretend that his train sleeping bunk is a spaceship while waiting for sleep, though no further specific references are made in the chapter.
Bloom County Edit
Some of the gang frequently played Star Trek: The Original Series, with Cutter John as James T. Kirk, Opus (and Steve Dallas briefly) as Spock, Portnoy as Montgomery Scott, and Hodge-Podge as Hikaru Sulu.
Later in the book, Randy Waterhouse worriedly compares having explained the strategy of his dotcom bubble company to a person he perceived to be a hick to a Federation scientist beaming down to a primitive planet and thoughtlessly teaching the locals how to build a phaser cannon. It's also remarked that while Waterhouse hates Star Trek and also people who don't hate it, he has seen every episode.
A few hundred pages later, Randy muses that it's hard for him to engage Goto Dengo, a captain of industry and personal friend of general Douglas McArthur, in chitchat, because you can hardly just ask if he has seen the latest episode of Star Trek: More Time-Space Anomalies.
Near the climax of the book a number of characters venture into a Phillipines jungle, the cannopy of which is said to emmit "a phantastic whistling noise, like a phaser on overload".
The Dresden Files Edit
Double Dexter by Jeff LindsayEdit
Fatal Judgment Edit
(Written by Irene Hannon) US Marshal and FBI agents are described as "working at warp speed". 
Flow My Tears, the Policeman Said Edit
The Girl who played with FireEdit
Lisbeth Salander is called mister Spock.
The Hardy Boys Edit
Star Trek has been referenced numerous times in The Hardy Boys novel series, published by Simon & Schuster, the company behind the Star Trek novels. Most recently in The Hardy Boys Undercover Brothers #25 Double Trouble, where Joe Hardy sarcastically compares his older brother, Frank, to "Mr. Spock", and most notable in The Hardy Boys #172 Trouble in Warp Space, in which the Joe's girlfriend gets a walk-on part in a new TV series called Warp Space, an obvious reference to Star Trek: Enterprise.
Hawk (The Quiet Professionals, book 2) Edit
(Written by Ronie Kendig) Boris Kolceki, a computer hacker, recalls Data singing about "tiny little life forms". 
Hidden Falls Edit
(Written by Olivia Newport) A man sees his son watching something on a sci fi channel and asks if it's Star Trek. The son replies that it's Battlestar Galactica.
The House of Night (Marked)Edit
Zoey, one of the main characters, admits to being a Star Trek fan, and had a Borg Invasion 4D hoodie.
I Love You, Beth CooperEdit
The Jungle: A Novel of the Oregon Files by Clive CusslerEdit
MacD says that the Oregon's op center is reminiscent of the Enterprise and that Juan's chair in the middle of it (which Juan referred to as the "Kirk Chair") is where Chris Pine sat, prompting Juan to realize he was too out-of-touch to know there'd been a new Trek movie.
The Killing StarEdit
In The Killing Star by Charles R. Pellegrino, the invaders use Star Trek as an example of why humans are dangerous (due to the show being human-centered).
Keith R.A. DeCandido authored one.
The Con Job by Matt ForbeckEdit
Hardison observes that concocting a sequel to Gavin Lee's book is as a much of a tease as the idea of new episodes of Mad Magazine (#115, Decem. At the end, he tells Parker that the place where the Star Trek: The Original Series cast had put their hands in the concrete of Grauman's Chinese Theater in Hollywood is sacred ground.
Night of the Living Trekkies Edit
A comedy-horror novel about a zombie outbreak at a Trek convention. The YouTube trailer for it says it is set at the "Botany Bay Hotel & Convention Center" and features a reporter named "Natasha Yar".
Omicron Ceti III Edit
The Onion Edit
The satirical newspaper The Onion frequently makes references to Star Trek. One of its recurring columnists, an obnoxious sci-fi fan named Larry Groznic, sometimes mentions the franchise - in addition to occasionally mentioning meetings with Trek actors such as John de Lancie and Marc Alaimo , he boasts in the October 15, 2001 issue of writing a crossover with Back to the Future in which Doc and Marty secretly assist Kirk and Spock in Star Trek IV: The Voyage Home  (evidently forgetting the resemblance Doc bears to someone of Kirk's acquaintance), while in the April 10, 2003 issue, in harshly criticizing someone for his decision not to learn Elvish, he wonders if that person would even bother to learn a language as simple and inelegant as Klingonese . The paper has also made light of Barack Obama's well-known status as a Trek fan - three weeks after the release of Star Trek (a video on its website showed a faux newscast  in which numerous Trekkies leave the theater with harsh words for the "fun, watchable" film) the front page of the May 26, 2009 issue included a picture  of Obama giving a press conference with fake Vulcan ears, with "Obama Addresses Nation Still Wearing Spock Ears" in a caption below, while in the December 9, 2009 issue, amid the uproar following the uninvited presence of a Virginia couple's at a state dinner, an "infographic"  revealed numerous other White House security breaches, including the accessing of sensitive information by thousands of people; this was blamed on the fact that Obama's passowrd, "NCC-1701", was not a terribly difficult one to crack.
Pale Kings and Princes by Robert B. ParkerEdit
Book 3 in The Nikki Boyd Files by Lisa Harris. A character is said to have attended a Star Trek convention with his girlfriend.
Quarry in the Black by Max Allan CollinsEdit
Leonard Nimoy is stumping for George McGovern during the tail end of the 1972 Presidential election, and Quarry frequently refers to him as Spock. When Nimoy refers to McGovern as his costar, Quarry has to be reminded that he's not speaking about William Shatner.
- See Redshirts
The Universal Union, Space Fleet, Captain Lucius Abernathy, Q'eeng, Anatoly Kerensky, Chief Medical Officer Hanson, and Chief Engineer West are all parallels of the United Federation of Planets, Starfleet, James T. Kirk, Spock, Pavel Chekov, Leonard McCoy and Montgomery Scott. When explaining why their lives are so dangerous, Jenkins puts up a picture of the Enterprise and says that they're living in a poorly-written TOS knockoff. Upon time-traveling back to 2012 Los Angeles, Brian Abnett says to Duvall that somebody has to be the redshirt.
Serge A. Storms novels of Tim DorseyEdit
Torpedo Juice Edit
The Big Bamboo Edit
When Elves AttackEdit
Shatnerquake is a novel by noted bizarro fiction author Jeff Burk. The story involves actor William Shatner being trapped at a convention at which he is forced into mortal combat against all the characters he has ever played, including multiple versions of James T. Kirk.
Snow Crash by Neal StephensonEdit
It is said one can't beam into the Metaverse like James T. Kirk, and later Hiro notes that most hackers have pictures of the starship Enterprise on their walls. Also, L. Bob Rife purchased the aircraft carrier Enterprise from the United States Navy and made it his own personal yacht.
Star Wolf Edit
A series of sci-fi novels by David Gerrold about a hard-luck starship in the middle of an interstellar war also intended to be a TV series at one point.
The Middle of NowhereEdit
Blood and FireEdit
A reworking of a Star Trek: The Next Generation episode rejected due to overarching homosexual thematics and an AIDS metaphor.
The new captain of the Star Wolf is said to have been previously posted on "The Big E," which is also said can't be risked on the front lines due to potential loss of morale if she's destroyed. A dead crewmember found on the Norway is named "M. Okuda."
Star Wreck: The Generation Gap Edit
This mass-market paperback was first released in 1990. It is a tongue-in-cheek parody of the Trek universe, written by Wisconsin native Leah Rewolinski, with illustrations by Harry Trumbore. Six sequels followed. The books mainly center upon spoofs of the TOS and TNG series, with books six and seven spoofing DS9 as well.
The seven released titles in the series were:
- Star Wreck: The Generation Gap (1990)
- Star Wreck II: The Attack of the Jargonites (1992)
- Star Wreck III: Time Warped: A Parody - Then, Now and Forever (1992)
- Star Wreck IV: Live Long and Profit : A Collection of Cosmic Capers (1993)
- Star Wreck V: The Undiscovered Nursing Home (1993)
- Star Wreck 6: Geek Space Nine (1994)
- Star Wreck 7: Space the Fido Frontier (1994)
The War Against The Chtorr Edit
A Day For DamnationEdit
This time travel novel by Michael Crichton novel features an introduction in which the supposed reality of some of the science of the book is discussed. At one point, the phrase "beam me up, Scotty" is used in relation to the concept of teleportation.
Turtles all the Way Down Edit
Novel by John Green who admits to being a fan of the franchise himself. The protagonist, Aza Holmes is a Trekkie.
A novel by Lev Grossman about a twentysomething who relates to the world through Star Trek and other references. The original cover featured the USS Enterprise (NCC-1701-D).
When A Heart StopsEdit
Book by Lynette Eason. At one point during the novel, a character's blood is said to run at warp speed through her veins.
By A. L. Shields. A character's eyebrow is said to rise like Mr. Spock's.