Note: the episodes are numbered according to production order (as opposed to airdate order).
Season 1: 1966-1967
Season 1, Episodes 00-01 – The Cage (unaired); Where No Man Has Gone Before
Season 1, Episodes 02-05 – The Corbomite Maneuver; Mudd’s Women; The Enemy Within; The Man Trap
Season 1, Episodes 06-09 – The Naked Time; Charlie X; Balance of Terror; What Are Little Girls Made Of?
Season 1, Episodes 10-13 – Dagger of the Mind; Miri; The Conscience of the King; The Galileo Seven
Season 1, Episodes 14-17 – Court Martial; The Menagerie, parts I and II; Shore Leave
Season 1, Episodes 18-21 – The Squire of Gothos; Arena; The Alternative Factor; Tomorrow is Yesterday
Season 1, Episodes 22-25 – The Return of the Archons; A Taste of Armageddon; Space Seed; This Side of Paradise
Season 1, Episodes 26-29 – The Devil in the Dark; Errand of Mercy; The City on the Edge of Forever; Operation: Annihilate!
Season 2: 1967-1968
Season 2, Episodes 01-04 – Catspaw; Metamorphosis; Friday’s Child; Who Mourns for Adonais?
Season 2, Episodes 05-08 – Amok Time; The Doomsday Machine; Wolf in the Fold; The Changeling
Season 2, Episodes 09-12 – The Apple; Mirror, Mirror; The Deadly Years; I, Mudd
Season 2, Episodes 13-16 – The Trouble with Tribbles; Bread and Circuses; Journey to Babel; A Private Little War
Season 2, Episodes 17-20 – The Gamesters of Triskelion; Obsession; The Immunity Syndrome; A Piece of the Action
Season 2, Episodes 21-23 – By Any Other Name; Return to Tomorrow; Patterns of Force
Season 2, Episodes 24-26 – The Ultimate Computer; The Omega Glory; Assignment: Earth
Season 3: 1968-1969
Season 3, Episodes 01-04 – Spectre of the Gun; Elaan of Troyius; The Paradise Syndrome; The Enterprise Incident
Season 3, Episodes 05-08 – And the Children Shall Lead; Spock’s Brain; Is There in Truth No Beauty?; The Empath
Season 3, Episodes 09-12 – The Tholian Web; For the World is Hollow and I Have Touched the Sky; Day of the Dove; Plato’s Stepchildren
Season 3, Episodes 13-16 – Wink of an Eye; That Which Survives; Let That Be Your Last Battlefield; Whom Gods Destroy… and a bonus
Season 3, Episodes 17-20 – The Mark of Gideon; The Lights of Zetar; The Cloud Minders; The Way to Eden
Season 3, Episodes 21-24 – Requiem for Methuselah; The Savage Curtain; All Our Yesterdays; Turnabout Intruder