- Playboy ranked all episodes of Star Trek that have ever been made, which is over 700.
- Two-parters were counted as one episode, so the list is actually under 700.
- The movies don't count, but the animated series does.
Archer and T'Pol bring back the Kir'Shara (Surak's artifact) that will lead to vast changes in the Vulcan world. T'Pol's Pa'nar Syndrome is cured by T'Pau.
12) “Scorpion,” Voyager, Season 3-4
Voyager must pass through Borg space, only to discover a new alien race that are even deadlier than the Borg.
7) “By Inferno's Light,” Deep Space Nine, Season 5
Gul Dukat aligns the Cardassians with the Dominion. The station must deal with a Changeling infiltrator.
2) “The Inner Light,” The Next Generation, Season 5
A space probe creates a telepathic tether to Picard and causes him to experience, in twenty-five minutes, a lifetime as a married man on a world that was destroyed a millennium ago.
1) “The City on the Edge of Forever,” The Original Series, Season 1
After accidentally overdosing on a powerful stimulant, Dr. McCoy becomes unbalanced and disappears through the Guardian of Forever, a newly discovered time portal on a remote planet. Kirk and Spock follow after learning that McCoy somehow changed history. Arriving in the 1930s, the duo meet Edith Keeler, a New York social worker who gives them a place to stay. As the days pass, and McCoy is nowhere to be seen, Kirk finds himself falling in love with Keeler... but Spock discovers that Keeler must die to restore the timeline
51) “Space Seed,” The Original Series, Season 1
The Enterprise discovers an ancient sleeper ship, the SS Botany Bay, which escaped from Earth's Eugenics Wars in the late 20th century. The genetically engineered passengers, led by war criminal Khan Noonien Singh, seize control of the Enterprise and attempt to destroy the ship. (This episode serves as the backstory to the second Star Trek film).
34) “The Trouble With Tribbles,” The Original Series, Season 2
A grTribbles – purring, limbless, and fertile – disrupt the exploitation of a disputed planet between the Klingons and Federation.
13) “Trials and Tribble-ations,” Deep Space Nine, Season 5
Darvin, a disgraced Klingon spy, travels back in time. The DS9 crew must prevent him from altering the timeline.
8) “The Best of Both Worlds,” The Next Generation, Season 3-4
Captain Picard is kidnapped by the Borg as they begin their invasion of Federation space.
Episode summaries taken from Wikipedia: 1, 2, 3, 4, 5, 6
Rest of list + commentary here.