I've put together a watching order for the Star Trek franchise. The list includes ENT, TOS, TAS, TNG, DS9, VOY, and all the films, save 11 as it is kinda in a different timeline. In the Kirk era, I've also included episodes from the fanseries Phase II.
The episodes are ordered in a mixture of release order, stardate, storyline, uniform appearance, and sometimes theme. If you have a suggestion for placement, feel free to say so. As of this moment, the list here is updated all the way through "The Way of the Warrior"
Broken Bow Fight or Flight/Strange New World Unexpected/Terra Nova The Andorian Incident/Breaking the Ice Civilization/Fortunate Son Silent Enemy/Cold Front Dear Doctor/Shadows of P'Jem Sleeping Dogs/Shuttlepod One Fusion/Rogue Planet Acquisition/Oasis Detained/Vox Sola Fallen Hero/Desert Crossing/Two Days and Two Nights Shockwave Carbon Creek/Minefield Dead Stop/A Night in Sickbay Marauders/The Seventh The Communicator/Singularity Vanishing Point/Precious Cargo The Catwalk/Dawn Stigma/Cease Fire Future Tense/Canamar The Crossing/Judgment Horizon/The Breach Cogenitor/Regeneration First Flight/Bounty The Expanse/The Xindi Anomaly/Extinction Rajiin/Impulse Exile/The Shipment Twilight/North Star Similitude/Carpenter Street Chosen Realm/Proving Ground Stratagem/Harbinger Hatchery/Doctor's Orders Azati Prime/Damage The Forgotten/E² The Council/Countdown/Zero Hour Storm Front/Home Borderland/Cold Station 12/The Augments The Forge/Awakening/Kir'Shara Daedalus/Observer Effect Babel One/United/The Aenar Affliction/Divergence Bound In a Mirror, Darkly Demons/Terra Prime The Cage Where No Man Has Gone Before The Corbomite Maneuver/Mudd's women The Enemy Within/The Man Trap The Naked Time/Charlie x Balance of Terror/What Are Little Girls Made Of? Dagger of the Mind/Miri The Conscience of the King/The Galileo Seven Court Martial/The Menagerie Shore Leave/The Squire of Gothos Arena/The Alternative Factor Tomorrow is Yesterday/The Return of the Archons A Taste of Armageddon/Space Seed This Side of Paradise/The Evil in the Dark Errand of Mercy/The City on the Edge of Forever Operation -- Annihilate!/Catspaw Metamorphosis/Friday's Child Who Mourns for Adonais?/Amok Time The Doomsday Machine/Wolf in the Fold The Changeling/The Apple Mirror, Mirror/The Deadly Years I, Mudd/The Trouble with Tribbles Bread and Circuses/Journey to Babel A Private Little War/The Gamesters of Triskelion Obsession/The Immunity syndrome A Piece of the Action/By Any other Name Return to Tomorrow/Patterns of Force The Ultimate Computer/The Omega Glory Assignment Earth/Spectre of the Gun Elaan of Troyius/The Paradise Syndrome The Enterprise Incident/And the Children Shall Lead Spock's Brain/Is There in Truth No Beauty? The Empath/The Tholian web For the World is Hollow and I Have Touched the Sky/Day of the Dove Plato's Stepchildren/Wink of an Eye That Which Survives/Let That Be Your Last Battlefield Whom Gods Destroy/The Mark of Gideon The Lights of Zetar/The Cloud Minders The Way to Eden/Requiem for Methuselah The Savage Curtain/All Our Yesterdays Turnabout Intruder/More Tribbles, More Troubles/The Infinite Vulcan Yesteryear/Beyond the Farthest Star/The Survivor The Lorelei Signal/One of Our Planets Is Missing/Mudd's Passion The Magicks of Megas-Tu/The Time Trap/The Slaver Weapon Once Upon a Planet/The Ambergris Element/The Jihad The Terratin Incident/The Eye of the Beholder/Bem Albatross/The Pirates of Orion The Practical Joker/How Sharper Than a Serpent's Tooth/The Counter-Clock Incident Come What May/In Harm's Way To Serve All My Days/World Enough and Time Blood and Fire Enemy: Starfleet/The Child Kitumba/Mind-Sifter The Motion Picture The Wrath of Khan The Search for Spock The Voyage Home The Final Frontier The Undiscovered Country Encounter at Farpoint The Naked Now/Code of Honor Haven /Where No One Has Gone Before The Last Outpost /Lonely Among Us Justice/The Battle Hide and Q /Too Short a Season The Big Goodbye/Datalore Angel One/11001001 Home Soil/When The Bough Breaks Coming of Age/Heart of Glory The Arsenal of Freedom/Symbiosis Skin of Evil/We'll Always Have Paris Conspiracy/The Neutral Zone The Child/Where Silence Has Lease Elementary, Dear Data/The Outrageous Okona The Schizoid Man/Loud As A Whisper Unnatural Selection/A Matter of Honor The Measure of A Man Extended Edition The Dauphin/Contagion The Royale/Time Squared The Icarus Factor/Pen Pals Q Who?/Samaritan Snare Up The Long Ladder/Manhunt The Emissary/Shades of Gray/Peak Performance Evolution/The Ensigns of Command The Survivors/Who Watches The Watchers? The Bonding/Booby Trap/The Enemy The Price/The Vengeance Factor The Defector/The Hunted The High Ground/Deja Q A Matter of Perspective/Yesterday's Enterprise The Offspring/Sins of the Father Allegiance/Captain's Holiday Tin Man/Hollow Pursuits The Most Toys/Sarek Manage a Troi/Transfigurations The Best of Both Worlds/Family Suddenly Human/Brothers Remember Me/Legacy Reunion/Future Imperfect Final Mission/The Loss Data' s Day/The Wounded Devil's Due/Clues First Contact/Galaxy's Child Night Terrors/Identity crisis The Nth Degree/Qpid The Drumhead/Half a Life The Host/The Mind's Eye/In Theory Redemption Darmok/Ensign Ro Silicon Avatar/Disaster/The Game Unification A Matter of Time/New Ground Hero Worship Violations/The Masterpiece Society Conundrum/Power Play Ethics/The Outcast Cause and Effect/The First Duty Cost of Living/The Perfect Mate Imaginary Friend/I Borg The Next Phase/The Inner Light Time's Arrow Realm of Fear/Man of the People Relics/Schisms True Q/Rascals A Fistful of Datas/The Quality of Life Chain of Command Emissary Past Prologue/A Man Alone/Babel Ship in a Bottle/Aquiel Captive Pursuit/Face of the Enemy Q-Less/Tapestry/Dax Birthright The Passenger/Move Along Home/The Nagus Starship Mine/Lessons Vortex/Battle Lines/The Storyteller The Chase/Frame of Mind/Suspicions Progress/Rightful Heir If Wishes Were Horses/Second Chances The Forsaken/Dramatis Personae Timescape/Duet Descent In the Hands of the Prophets/The Homecoming/The Circle/The Siege Liasons/Interface The Gambit Invasive Procedures/Phantasms Cardassians/Dark Page Melora/Attached Rules of Acquisition/Force of Nature Necessary Evil/Inheritance Second Sight/Parallels Sanctuary/Rivals The Pegasus/These Are The Voyages The Alternate/Homeward Sub Rosa/Armageddon Game Lower Decks/Whispers Thine Own self/Paradise Masks/Shadowplay Eye of the Beholder/Playing God Genesis/Profit and Loss Journey's End/Blood Oath Firstborn/Bloodlines The Marquis Emergence/The Wire Preemptive Strike Crossover/The Collaborator/Tribunal/The Jem' Hadar All Good Things... The Search The House of Quark/Equilibrium Second Skin/The Abandoned Civil Defense/Meridian Defiant/Fascination Past Tense Caretaker Parallax/Time and Again Life Support/Heart of Stone Phage/Destiny/The Cloud Prophet Motive/Visionary Eye of the Needle/Distant Voices Through the Looking Glass/Ex Post Facto/Emanations Star Trek: Regeneration (Generations) Prime Factors/State of Flux/Heroes and Demons Improbable Cause/The Die is Cast Cathexis/Faces Explorers/Jetrel Family Business/Learning Curve Shakaar/Facets Projections/Elogium The Adversary/Twisted The 37's/Initiations/Non Sequitur The Way of the Warrior