This is a list of fictional materials from the science fiction universe of Star Trek. Like other aspects of stories in the franchise, some were recurring plot elements from one episode or series to another.
Star Trek technical manuals indicate that transparent aluminum is used in various fittings in starships, including exterior ship portals and windows. It was notably mentioned in the 1986 film Star Trek IV: The Voyage Home. Panels of ultra-thick acrylic glass were needed to construct water tanks within their ship's cargo bay for containing two humpback whales and tonnes of water. However, the Enterprise crew, without money appropriate to the period, found it necessary to barter for the required materials. Chief Engineer Scott exchanged the chemical formula for transparent aluminum for several sheets of an adequate substitute from a manufacturer, PMMA - when Dr. McCoy castigates him for potentially disrupting the timeline, the engineer responds, "How do we know he didn't invent the thing?" (In the novelization of the film, Scotty is aware that Nichols was in the its "inventor", and concludes that his giving of the formula is a predestination paradox.) The substance is described as being as transparent as glass while possessing the strength and density of high-grade aluminum. André Bormanis has concluded that the material would not be a good conductor of electricity.
The fictional term is now being used as a real world descriptor for a newly discovered transient state of matter, "transparent aluminium" bombarded with high levels of x-ray radiation, which temporarily becomes transparent to X-rays of the same wavelength (13.5 nm).
Trellium-D, shown in Star Trek: Enterprise, was an alloy used in the Delphic Expanse as a protection against spatial anomalies there. It had unusual effects on Vulcan physiology, and became a recurring plot element in the third season of Star Trek: Enterprise, exploring the theme of drug addiction.
Other materials were occasionally mentioned in the scripts, such as nitrium, a radiation-resistant material.
Dilithium crystals, in all Star Trek series, were shown to be an essential component for a starship's faster than light drive, or warp drive, since they were necessary to regulate the matter-antimatter reactions needed to generate the required energy. Dilithium was frequently featured in the original series as a scarce resource. By the time in which the later series were set, dilithium could be synthesized.
Trilithium is a material used in a star-destroying weapon in Star Trek Generations. This is due to the fact that Trilithium is termed as a "nuclear inhibitor", which is believed to be any substance which interferes with nuclear reactions. In the film, Trilithium is known to be capable, when used to its full potential, of stopping all fusion within a star, thereby collapsing the star and destroying everything within its solar system via a shock wave.
Latinum featured in many episodes of Deep Space Nine as a medium of exchange used by Ferengis and others. It was a liquid usually traded as "gold-pressed latinum"; once the latinum was extracted, the gold was discarded.
Tholian silk was a valuable fabric mentioned in multiple series.
Bio-mimetic gel is a volatile substance with medical applications. It is also highly sought after for use in illegal activities, such as genetic experimentation and biological weapons development. As such, its use is strictly regulated by the United Federation of Planets, and sale of the substance is prohibited. The substance was first mentioned in an episode of Star Trek: The Next Generation, and was used as a plot element in several episodes of Star Trek: Deep Space Nine.
Kironide is a mineral by which, in Star Trek: The Original Series, in the episode Plato's Stepchildren, the Platonians (the inhabitants of the planet Platonius) have telekinetic powers including the ability to levitate from consuming plants containing the mineral kironide. 
Protomatter is a key component of the Genesis Device prototype--an experimental terraformation device introduced in Star Trek II: The Wrath of Khan. Protomatter is presented as a very unstable substance that, due to its instability, is considered unethical for usage in scientific research. The substance is used as a plot device to compare David Marcus with his father, James T. Kirk, both of whom, in Lieutenant Saavik's words, "changed the rules"--David Marcus in using the forbidden protomatter, and James T. Kirk in "cheating" to win the Kobayashi Maru test. The inclusion of protomatter ultimately results in both the accelerated maturation of the regenerated Spock during his stay on the Genesis planet, and the planet's subsequent explosion into an asteroid belt.
Red matter was a red, liquid material introduced in Star Trek (the 2009 film) which was able to create a black hole when uncontained. Spock attempted to use it to stop a massive, galaxy-threatening supernova, but the resultant black hole caused his own ship and a Romulan mining vessel to travel back in time. Later in the film, the antagonist Nero used it to destroy the planet Vulcan. Shortly after, the future Spock's ship containing the red matter was used to destroy Nero's Romulan mining vessel.
Tritanium is also a metallic mineral used in the construction of star ships in the MMORPG EVE Online. In the EVE universe, tritanium is a versatile material and is the primary material used in the construction of virtually all star ships and star ship components. It is described as being unstable at atmospheric temperatures, and thus is only used in constructing objects intended to stay in space permanently.