The io9 website has a list of the top 100 Star Trek episodes, encompassing all six series.
I don’t necessarily agree with all the rankings, and others I haven’t seen (I paid less attention to Deep Space 9, Voyager and Enterprise than the original and The Next Generation), but I spotlight my favorites:
What makes for a great Star Trek episode? Obviously, the fun quotient has to be high, and there need to be awesome character moments. But I’d argue that a really notable Trek story explores some ideas, or some ethical quandaries, in a way that sticks with you after you’re done watching. If one thing has defined Trek throughout its run, it’s that …
99) Day of the Dove (Star Trek) – An alien entity wants the Enterprise crew and some Klingons to slaughter each other, and Kirk has nearly as much trouble with his own crew as with the “enemy.”
Michael Ansara (the Klingon) had one of the great voices in TV in his day. This is one of the few watchable episodes of the disastrous third season. (Another appears later.)
89) Court Martial (Star Trek) – Kirk is put on trial, and along the way he shows what it really takes to command a starship. …
87) Déjà Q (Star Trek: The Next Generation) – Q has lost his powers, and now he’s learning to cope with being human. If he can survive the wrath of Guinan, that is.
I am not really a fan of the Q character, because it strikes me as a lazy plot device. (Hey! Let’s create an all-powerful being!) However, there is a cameo by Corbin Bernsen, when every TV viewer knew him as the womanizing lawyer on “L.A. Law,” and he was fantastic in his brief part.
85) Little Green Men (Star Trek: Deep Space Nine) – Quark gets stranded on mid-20th century Earth, and for once even he can’t figure out how to profit from this, in a hilariously weird episode.
81) The Enemy Within (Star Trek) – The one where Kirk gets split into good and evil versions by a transporter accident — Richard Matheson’s script manages to get into some thorny questions about the nature of evil.
79) I, Mudd (Star Trek) – The most famous rogue in Star Trek has landed in a great spot — surrounded by beautiful androids who cater to his every whim. Except that he can’t leave.
Harcourt Fenton Mudd might be the only non-regular character from the original series to have appeared in more than one episode. His first appearance, “What Are Little Girls Made Of,” was considered as the pilot after the original pilot, “The Cage,” was rejected by NBC. This is a pretty silly episode, but entertaining, in addition to being many viewers’ introduction to the Liar’s Paradox:
76) Wolf in the Fold (Star Trek) – Mr. Scott is accused of being a serial killer… but the truth is a lot more bizarre.
This isn’t really one of my favorites; I bring it up to spotlight the killer (spoiler alert!), Platteville’s own John Fiedler, the voice of Piglet:
73) Family (Star Trek: The Next Generation) – This episode is revolutionary, purely because it shows the consequences of a big “event” episode — Picard is still shaken by his experiences with the Borg, when he goes home to visit his family.
71) A Piece of the Action (Star Trek) – One of many “visiting Earth’s past on another planet” episodes, this is the funniest and also the most trenchant. Kirk and friends have to outwit a whole planet of gangsters, while teaching them the arcane game of Fizzbin.
70) Sarek (Star Trek: The Next Generation) – Peter S. Beagle wrote this episode where Spock’s father reappears, and he’s not the Vulcan he used to be — a bittersweet exploration of aging and loss.
67) Errand of Mercy (Star Trek) – The first Klingon episode is also the most daring, as Kirk is portrayed as being nearly as warlike as his foes, in the face of godlike pacifist aliens.
62) Cause and Effect (Star Trek: The Next Generation) – The one where the Enterprise keeps blowing up over and over. The most explosive, bewildering time loop ever.
60) Shore Leave (Star Trek) – One of the goofiest original-series episodes also has a major dark side, as the crew arrives on a planet where anything they imagine can become real. Anything.
55) The Pegasus (Star Trek: The Next Generation) – Riker’s long-buried secret comes to light, and he’s forced to lie to Captain Picard.
53) The Conscience of the King (Star Trek) – This episode about a Shakespearean actor who may be a legendary mass murderer is also our first glimpse of the flaws in Trek‘s perfect future.
52) Relics (Star Trek: The Next Generation) – Old Starfleet engineers never die — they just come back decades later, eager to tinker with another warp engine.
50) I Borg (Star Trek: The Next Generation) – Another episode with a guest star who poses a huge ethical question — the Enterprise finds a disconnected Borg drone, and tries to turn him into a weapon.
48) The Enterprise Incident (Star Trek) – Kirk and Spock pull an elaborate hustle on the Romulans, in an episode that shows just how unethical our heroes are prepared to be.
43) Obsession (Star Trek) – Kirk’s judgment is called into question when he becomes fixated on revenge, showing once again just how dangerous an out-of-control captain can be.
39) Journey to Babel (Star Trek) – Most notable for introducing us to Spock’s parents, this episode also shows a Federation diplomatic mission gone horribly wrong.
36) Galileo Seven (Star Trek) – A shuttlecraft full of people is stranded on a planet, and it appears that not all of them can survive. Good thing Spock is in charge, and he has zero hesitation about making the tough call… Right?
34) The Drumhead (Star Trek: The Next Generation) – An Admiral subjects the Enterprise to an inquisition, and starts finding conspiracies behind every bulkhead, providing an object lesson in the dangers of paranoia.
32) Trials and Tribble-ations (Star Trek: Deep Space Nine) – One of several time-travel episodes, this one sends Sisko’s officers back to the original series episode “The Trouble With Tribbles,” and provides a great love letter to Trek‘s history.
30) Yesteryear (Star Trek: The Animated Series) – Spock travels back in time and saves himself as a young boy on Vulcan, in an episode that reveals a lot about Spock’s life.
27) Where No Man Has Gone Before (Star Trek) – The second Star Trek pilot is the best, facing Kirk with an impossible choice: condemn his friend to death, or risk his entire ship.
25) The Offspring (Star Trek: The Next Generation) – Data creates an android daughter for himself, but some miracles are too great to last.
22) Tapestry (Star Trek: The Next Generation) – Picard is dying of an old wound caused by his recklessness, so Q shows him what his life would be like if he’d played it safe.
21) Arena (Star Trek) – Kirk faces two impossible challenges: making a weapon from scratch, and upholding his values in the face of a murderous Gorn.
20) Measure of a Man (Star Trek: The Next Generation) – Putting Data on “trial” to see if he’s a person raises fascinating questions, but the best part is Riker’s total ruthlessness as prosecutor.
19) Yesterday’s Enterprise (Star Trek: The Next Generation) – The Enterprise finds itself in an alternate universe, and restoring the original timeline will come at a high cost.
18) The Doomsday Machine (Star Trek) – Kirk faces the ultimate weapon, but his real nightmare is an unhinged superior officer taking command of the Enterprise.
Favorite episode number 1B, because only Kirk would do this …
… and of course his crew would follow his orders. This episode proves why Kirk is the ultimate Star Trek captain.
16) Devil in the Dark (Star Trek) – The classic Star Trek scenario: a story in which the “monster” is misunderstood, and ignorant humans are the real danger.
15) Space Seed (Star Trek) – The only Trek episode to get a movie sequel, this story introduces a suave former dictator who’s a perfect foil for Kirk.
14) The Corbomite Maneuver (Star Trek) – This episode isn’t named after the villain or the McGuffin, but after Kirk’s cunning gambit — with good reason. Never play poker with Kirk.
This wasn’t the pilot, and it wasn’t the first episode, but it was the first episode to be filmed, after the rejected pilot “The Cage” and the approved pilot “Where No Man Has Gone Before.” It would have been a good pilot episode.
11) Chain of Command (Star Trek: The Next Generation) – Picard is captured by a ruthless Cardassian torturer — and gets pushed to his limits.
There is much more to this episode than that description. Picard is captured during a secret mission; his replacement as captain is more demanding, and actually relieves Riker of duty because Riker won’t follow his orders without question. I’ve read some thought that the series should have used this episode to replace Picard with his replacement, perhaps because those viewers prefer a series more like Deep Space Nine, where the characters have to live with each other, but don’t necessarily like each other.
10) Mirror, Mirror (Star Trek) – Meeting alternate crewmembers, including Bearded Spock, is cool — but the fascinating part is seeing our heroes try to pretend to be barbarians.
As main-universe Spock points out at the end, it is easier for civilized men to act like barbarians than it is for barbarians to act like civilized men.
9) All Good Things (Star Trek: The Next Generation) – The best Q story sees Picard tested at three points in his life, with the whole universe in the balance.
8) The Inner Light (Star Trek: The Next Generation) – Picard lives a whole life on a doomed planet, and becomes a living memorial, with just a flute as souvenir.
6) The Trouble with Tribbles (Star Trek) – The funniest Trek, it also faces Kirk with the most insidious threat: an organism that’s born pregnant.
2) The Best of Both Worlds (Star Trek: The Next Generation) – The Borg turn Picard into their mouthpiece, and our heroes nearly lose.
1) Balance of Terror (Star Trek) – Kirk’s battle of wits with a Romulan is spellbinding, but so is the exploration of prejudice, and the idea that noble people fight on both sides.
Favorite episode number 1A.
There are a few episodes from the first three series not on their list that are on my list. “A Taste of Armageddon” has Kirk ending an interplanetary war by escalating it. (Again, only Kirk can pull this off.)
“The Immunity Syndrome” has the Enterprise inside a giant single-celled creature that already destroyed another starship and solar system.
“Patterns of Force” has Kirk trying to undo the hideous mistake of a Federation functionary — unifying a divided planet through the Nazi Germany model. It’s not as funny as “A Piece of the Action,” but it has some great Kirk/Spock moments:
One episode from The Animated Series would have worked in any of the live-bodies series — “Beyond the Farthest Star,” where the Enterprise encounters an abandoned ship possessed by an alien that they get rid of by pointing the Enterprise at a black hole at high speed.
The Next Generation started with arguably its worst season, redeemed by two episodes — “Conspiracy,” where a truly creepy creature takes over its hosts’ bodies; and “The Neutral Zone,” where the Romulans make their reappearance. The former is in the spirit of one of the better original-series episodes, with a nice touch at the end, a ’50s-style To Be Continued??? ending.
You have to ignore the “We have eliminated need” self-satisfaction that belies human nature in the latter, but it’s still a very good episode.
I’m not sure much is in common with all these episodes. For me, the best Star Trek episodes combine action, whether on a planet or on the ship, and the characters doing the right thing despite fear, anger or other forces. In most of these episodes the byplay between characters stands out. “Where No Man Has Gone Before” begins with Kirk and Spock playing chess, and Spock about to win until Kirk makes an unexpected, unorthodox move. (Surprised?) “Trials and Tribble-ations” includes Odo’s withering sarcasm about Klingons’ destroying the tribbles’ home world, which he calls “another glorious chapter in Klingon history,” asking Worf, “Tell me, do they still sing songs about The Great Tribble Hunt?”
99) Day of the Dove (Star Trek) – An alien entity wants the Enterprise crew and some Klingons to slaughter each other, and Kirk has nearly as much trouble with his own crew as with the “enemy.”
89) Court Martial (Star Trek) – Kirk is put on trial, and along the way he shows what it really takes to command a starship. …
87) Déjà Q (Star Trek: The Next Generation) – Q has lost his powers, and now he’s learning to cope with being human. If he can survive the wrath of Guinan, that is.
85) Little Green Men (Star Trek: Deep Space Nine) – Quark gets stranded on mid-20th century Earth, and for once even he can’t figure out how to profit from this, in a hilariously weird episode.
81) The Enemy Within (Star Trek) – The one where Kirk gets split into good and evil versions by a transporter accident — Richard Matheson’s script manages to get into some thorny questions about the nature of evil.
79) I, Mudd (Star Trek) – The most famous rogue in Star Trek has landed in a great spot — surrounded by beautiful androids who cater to his every whim. Except that he can’t leave.
76) Wolf in the Fold (Star Trek) – Mr. Scott is accused of being a serial killer… but the truth is a lot more bizarre.
73) Family (Star Trek: The Next Generation) – This episode is revolutionary, purely because it shows the consequences of a big “event” episode — Picard is still shaken by his experiences with the Borg, when he goes home to visit his family.
71) A Piece of the Action (Star Trek) – One of many “visiting Earth’s past on another planet” episodes, this is the funniest and also the most trenchant. Kirk and friends have to outwit a whole planet of gangsters, while teaching them the arcane game of Fizzbin.
70) Sarek (Star Trek: The Next Generation) – Peter S. Beagle wrote this episode where Spock’s father reappears, and he’s not the Vulcan he used to be — a bittersweet exploration of aging and loss.
67) Errand of Mercy (Star Trek) – The first Klingon episode is also the most daring, as Kirk is portrayed as being nearly as warlike as his foes, in the face of godlike pacifist aliens.
60) Shore Leave (Star Trek) – One of the goofiest original-series episodes also has a major dark side, as the crew arrives on a planet where anything they imagine can become real. Anything.
55) The Pegasus (Star Trek: The Next Generation) – Riker’s long-buried secret comes to light, and he’s forced to lie to Captain Picard.
53) The Conscience of the King (Star Trek) – This episode about a Shakespearean actor who may be a legendary mass murderer is also our first glimpse of the flaws in Trek‘s perfect future.
52) Relics (Star Trek: The Next Generation) – Old Starfleet engineers never die — they just come back decades later, eager to tinker with another warp engine.
50) I Borg (Star Trek: The Next Generation) – Another episode with a guest star who poses a huge ethical question — the Enterprise finds a disconnected Borg drone, and tries to turn him into a weapon.
48) The Enterprise Incident (Star Trek) – Kirk and Spock pull an elaborate hustle on the Romulans, in an episode that shows just how unethical our heroes are prepared to be.
43) Obsession (Star Trek) – Kirk’s judgment is called into question when he becomes fixated on revenge, showing once again just how dangerous an out-of-control captain can be.
39) Journey to Babel (Star Trek) – Most notable for introducing us to Spock’s parents, this episode also shows a Federation diplomatic mission gone horribly wrong.
36) Galileo Seven (Star Trek) – A shuttlecraft full of people is stranded on a planet, and it appears that not all of them can survive. Good thing Spock is in charge, and he has zero hesitation about making the tough call… Right?
34) The Drumhead (Star Trek: The Next Generation) – An Admiral subjects the Enterprise to an inquisition, and starts finding conspiracies behind every bulkhead, providing an object lesson in the dangers of paranoia.
32) Trials and Tribble-ations (Star Trek: Deep Space Nine) – One of several time-travel episodes, this one sends Sisko’s officers back to the original series episode “The Trouble With Tribbles,” and provides a great love letter to Trek‘s history.
30) Yesteryear (Star Trek: The Animated Series) – Spock travels back in time and saves himself as a young boy on Vulcan, in an episode that reveals a lot about Spock’s life.
27) Where No Man Has Gone Before (Star Trek) – The second Star Trek pilot is the best, facing Kirk with an impossible choice: condemn his friend to death, or risk his entire ship.
25) The Offspring (Star Trek: The Next Generation) – Data creates an android daughter for himself, but some miracles are too great to last.
22) Tapestry (Star Trek: The Next Generation) – Picard is dying of an old wound caused by his recklessness, so Q shows him what his life would be like if he’d played it safe.
21) Arena (Star Trek) – Kirk faces two impossible challenges: making a weapon from scratch, and upholding his values in the face of a murderous Gorn.
20) Measure of a Man (Star Trek: The Next Generation) – Putting Data on “trial” to see if he’s a person raises fascinating questions, but the best part is Riker’s total ruthlessness as prosecutor.
19) Yesterday’s Enterprise (Star Trek: The Next Generation) – The Enterprise finds itself in an alternate universe, and restoring the original timeline will come at a high cost.
18) The Doomsday Machine (Star Trek) – Kirk faces the ultimate weapon, but his real nightmare is an unhinged superior officer taking command of the Enterprise.
16) Devil in the Dark (Star Trek) – The classic Star Trek scenario: a story in which the “monster” is misunderstood, and ignorant humans are the real danger.
15) Space Seed (Star Trek) – The only Trek episode to get a movie sequel, this story introduces a suave former dictator who’s a perfect foil for Kirk.
14) The Corbomite Maneuver (Star Trek) – This episode isn’t named after the villain or the McGuffin, but after Kirk’s cunning gambit — with good reason. Never play poker with Kirk.
11) Chain of Command (Star Trek: The Next Generation) – Picard is captured by a ruthless Cardassian torturer — and gets pushed to his limits.
9) All Good Things (Star Trek: The Next Generation) – The best Q story sees Picard tested at three points in his life, with the whole universe in the balance.
1) Balance of Terror (Star Trek) – Kirk’s battle of wits with a Romulan is spellbinding, but so is the exploration of prejudice, and the idea that noble people fight on both sides.
Steve Prestegard.com: The Presteblog 
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