This page lists the entire series's episodes for all three seasons.
Unaired Pilot
The Cage
Season One
The Man Trap Charlie X Where No Man Has Gone Before The Naked Time The Enemy Within Mudd's Women What Are Little Girls Made Of? Miri Dagger of the Mind The Corbomite Maneuver The Menagerie, Part I The Menagerie, Part II The Conscience of the King Balance of Terror Shore Leave The Galileo Seven The Squire of Gothos Arena Tomorrow is Yesterday Court-Martial The Return of the Archons Space Seed A Taste of Armageddon This Side of Paradise The Devil in the Dark Errand of Mercy The Alternative Factor The City on the Edge of Forever Operation-Annihilate!
Season Two
Amok Time Who Mourns for Adonais? The Changeling Mirror, Mirror The Apple The Doomsday Machine Catspaw I, Mudd Metamorphosis Journey to Babel Friday's Child The Deadly Years Obsession Wolf in the Fold The Trouble With Tribbles The Gamesters of Triskelion A Piece of the Action The Immunity Syndrome A Private Little War Return to Tomorrow Patterns of Force By Any Other Name The Omega Glory The Ultimate Computer Bread and Circuses Assignment: Earth
Season Three
Spock's Brain The Enterprise Incident The Paradise Syndrome And the Children Shall Lead Is There In Truth No Beauty? Spectre of the Gun Day of the Dove For the World Is Hollow and I Have Touched the Sky The Tholian Web Plato's Stepchildren Wink of an Eye The Empath Elaan of Troyius Whom Gods Destroy Let That Be Your Last Battlefield The Mark of Gideon That Which Survives The Lights of Zetar Requiem For Methuselah The Way to Eden The Cloud Minders The Savage Curtain All Our Yesterdays Turnabout Intruder
My all time favorite episodes are: "Journey to Babel", "Balance of Terror", "Opperation-Annihilate", and "Amok Time". These episodes all kick some serious butt!