The Jefferies Tubes are named after Matt Jefferies, art director of TOS and designer of the original Starship Enterprise (both the interior and exterior).
Both Khan Noonien Singh and Dr. Noonien Soong (of TOS and TNG respectively) were named for a childhood friend of Gene Roddenberry. This no doubt comes as a relief to know if you were trying to figure out why their names were so similar.
The names of Clare Raymond's descendants in the Season 1 episode "The Neutral Zone" are William Hartnell, Patrick Troughton, Jon Pertwee, Tom Baker, Peter Davidson and Colin Baker. Save for one misspelling, these are the names of the first six actors to play The Doctor.
The Borg are one to The Cybermen. The title of their debut lampshades this by titling it "Q Who".
In one episode they mentioned a sonic screwdriver.
Several anime fans in the production staff sneaked references in:
One of the most blatant were the "exocomp" robots from "The Quality of Life". Word of God admits that their design was inspired by the Dirty Pair's Robot Buddy, Nammo. Kei and Yuri from the same series are named on various props.
"Kei-ee, Yur-ee..." is used as the beginning of a Ferengi access code in one episode.
The Enterprise has a sister ship called the Yamato, but this is actually a coincidence; they are both named after the same historic ship.
On the other hand, that the victims of radiation bombardment by an alien ship in "Final Mission" were named the Gamelans is almost certainly not coincidence.
In Season 2's "The Icarus Factor", Riker and his dad fight in an Anbo-jyutsu arena◊ decorated with Japanese characters. Some writing is stuff you'd expect — "water", "air", "fire", etc., but a wall hanging reads "Urusai [sic] Yatsura", and you can see names of the main characters, Lum and Ataru, written on the floor if you watch carefully. "Yuri" is written on the side, another reference to Dirty Pair.
In "The Most Toys", trader Kivas Fajo is from Tomobiki City, and attended the University of Oneamisu.
In "The Price", Devinoni Ral studied at Oneamisu Campus.
There is a linked pair of shout outs involving Star Trek and Seaquest DSV. In one TNG episode, an onscreen computer readout lists the service record of a crewman to have included the "USS Seaquest". In one Seaquest episode, an alien falls to its death next to a memorial commemorating the launch of the "Nomad" probe (referencing a probe that appeared in TOS).
"The Magnificent Ferengi" was a homage to The Magnificent Seven. Also, in one episode, the characters recite the first two lines of the Edwin Starr song "War".
In the pilot, Bashir borrows Odo's hand for some impromptu first aidan allusion to the film M* A* S* H, in which the same thing happens to Rene Auberjonois' character.
There is also of course the well known Shout-Out in the episode "Trials and Tribble-ations" where the two officers that Temporal Investigations sent to investigate Sisko et al.'s time traveling had names that were anagrams of "Mulder" and "Scully."
A kiosk listing businesses on the Promenade contained an entry for "Tom Servo's Used Robots," a reference to the character from Mystery Science Theater 3000.
The character "Morn" is largely a background character in Quark's bar; his name is an anagram of "Norm," in homage to another familiar barfly, from Cheers.
Lounge singer Vic Fontaine is a tribute to Frank Sinatra right down to having an episode that is basically a tribute to Ocean's Eleven. And What Could Have Been: They even had Frank Sinatra, Jr. in mind for the role (but he didn't want the partnote he wanted to be on the show, but only if he could play an alien).
As revealed in "The House of Quark", Quark's father's name is Kheldar. Kheldar is also the real name of Silk, the main Drasnian character in The Belgariad. The Drasnians, like the Ferengi, have a Hat of being devious merchants.
The Okudagram graphics (created by Mike Okuda) seen in the modern Star Trek series and films are loaded with references to people and other science fiction shows and characters. Another source are the ship dedication plaques located on the bridges of Starfleet next to the turbolift. The admirals, engineers and so on listed on them are the production staff for that series. Several ship mottoes found on the plaques are Shout-Outs as well; for example, the official motto of Excelsior is "No matter where you go, there you are." The "Most Wanted" list in Odo's office also featured photos of production staff.
In "Paradise Lost", when listing off the officers Sisko knows who are assigned to security work on Earth, all of them have the names of major characters from Catch22.
The Adventures of Captain Proton! Dr Chaotica wears identical clothing to Ming the Merciless, Proton's rocket ship has clear Flash Gordon influences, Satan's Robot is the "Republic Robot", an overused prop in various Republic Serials including ''Mysterious Doctor Satan'', while Proton's leather jacket with jetpack controls are the same as those used by Commando Cody.
In the episode "The Omega Directive", Seven of Nine sets up a system for capturing the Omega particle, and refers to the crew by numbers. The person who is most unhappy with this arrangement is the one assigned the number Six of Ten.
The episode "Flesh and Blood" had a brief reference to an alien race called the Ovions, who were described as hexapods. Ovions were an insect race in the Battlestar Galactica episode "Saga of a Star World".
In the teaser of "Zero Hour", the Xindi Reptilians eat live mice in a clear homage to the miniseries V.
In the series premiere, "Broken Bow", Admirals Forrest, Leonard and Williams are shout-outs to DeForest Kelley, Leonard Nimoy and William Shatner, respectively, who, of course, played McCoy, Spock and Kirk in TOS. Admiral Forrest, named after Kelley, had the most screen time throughout the series, most likely because Kelley had died in 1999, just a year or so before production began.
In the season 1 episode "Oasis," Trip sarcastically stretches the like "What do you do then? Program a holographic doctor?" *cough* Star Trek: Voyager *cough*.
Ridiculously Human Robots are called "synths," there is widespread hatred and paranoia of them, and their origin is a place called the Daystrom Institute, sometimes referred to as simply "the Institute." We've seen synths from the Institute somewhere else before, haven't we!
The episode title "Maps and Legends" is named after showrunner Michael Chabon's collection of sixteen essays. He defends genre literature in some of them (which includes Science Fiction), and we learn in this episode that Dr. Agnes Jurati is a fan of sci-fi author Isaac Asimov.
Elnor could be transported to Middle-earth, and he would seamlessly blend into that world because he's basically an Elf (Romulans are Space Elves, after all). The media frequently compared him to Legolas because he's long-haired, Elfeminate and has an agile, graceful fighting style. Elnor's name is similar to Elrond, and in Sindarin, "Elnor" means "Star-Run." note Showrunner Michael Chabon deliberately gave the character an Elvish name◊ that is a close approximation of "Star-Trek." The Qowat Milat monastery where he grew up is an Arboreal Abode situated in a forest which looks virtually identical to Rivendell, as the foliage and the late afternoon/early evening sunlight appear to be in a perpetual autumn setting. Elnor pledging his sword to Picard's quest and joining the latter's ragtag crew is akin to Legolas joining the Fellowship of the Ring, and their respective missions are extremely dangerous with little hope of success.
The planet Vashti shares its name with the Persian queen from the Book of Esther who disobeyed her drunk husband's command to "show her beauty" (i.e. appear naked) in front of him and his male guests at a banquet. Feminists interpret Vashti's defiance to be heroic because she stands up for herself despite knowing she'll be punished for going against her culture's patriarchal and misogynist values, which parallels the all-female Qowat Milat sect's refusal to bow down to the oppression of the Tal Shiar, who strictly enforces conformity in Romulan society and eliminates any Cultural Rebel.
An artifact left behind by an ancient but extinct civilization warns of annihilation by synthetics via a vision. Mind melds are used to then convey that vision from person to person, and may be the most effective way to do so. Sounds a lot like the Prothean beacon warning of the Reaper invasion.
In "Broken Pieces", Picard cites Don Quixote during his briefing with Admiral Clancy after she admits he was right.