Episodes listed here are episodes which ARE NOT in the canon, the rest of Star Trek is in the canon.
The Original Series:
S1E2 "Charlie X"
S1E4 "The Naked Time"
S1E5 "The Enemy Within"
S1E6 "Mudd's Women"
S1E7 "What Little Girls Are Made Of"
S1E8 "Miri"
S1E15 "Shore Leave"
S1E17 "The Squire of Gothos"
S1E18 "Arena"
S1E21 "The Return of The Archons"
S1E24 "This Side of Paradise"
S1E25 "The Devil in the Dark"
S1E26 "Errand of Mercy"
S1E27 "The Alternative Factor"
S1E28 "Operation--Annihilate!"
S2E2 "Who Mourns for Adonais?"
S2E3 "The Changeling"
S2E5 "The Apple"
S2E7 "Catspaw"
S2E8 "I, Mudd"
S2E9 "Metamorphosis"
S2E11 "Friday's Child"
S2E12 "The Deadly Years"
S2E14 "Wolf in the Fold"
S2E15 "The Trouble With Tribbles"
S2E16 "The Gamesters of Triskelion"
S2E17 "A Piece of the Action"
S2E20 "Return to Tomorrow"
S2E21 "Patterns of Force"
S2E22 "By Any Other Name"
S2E23 "The Omega Glory"
S2E25 "Bread and Circuses"
S2E26 "Assignment: Earth"
S3E1 "Spock's Brain"
S3E4 "And the Children Shall Lead"
S3E5 "Is There In Truth No Beauty?"
S3E6 "Spectre of the Gun"
S3E7 "Day of the Dove"
S3E8 "For the World Is Hollow and I Have Touched the Sky"
S3E10 "Plato's Stepchildren"
S3E11 "Wink of an Eye"
S3E13 "Elaan of Troyius"
S3E14 "Whom Gods Destroy"
S3E15 "Let That Be Your Last Battlefield"
S3E16 "The Mark of Gideon
S3E17 "That Which Survives"
S3E18 "The Lights of Zetar"
S3E19 "Requiem for Methuselah"
S3E20 "The Way to Eden"
S3E22 "The Savage Curtain"
The Next Generation:
S1E4 "Code of Honor"
S1E5 "The Last Outpost"
S1E7 "Lonely Among Us"
S1E8 "Justice
S1E11 "Haven"
S1E12 "The Big Goodbye"
S1E14 "Angel One"
S1E16 "Too Short a Season"
S1E17 "When the Bough Breaks"
S1E18 "Home Soil"
S1E24 "We'll Always Have Paris"
S1E25 "Conspiracy"
S1E26 "The Neutral Zone"
S2E2 "Where Silence Has Lease"
S2E4 "The Outrageous Okona
S2E5 "Loud as a Whisper"
S2E6 "The Schizoid Man"
S2E7 "Unnatural Selection"
S2E12 "The Royale"
S2E17 "Samaritan Snare"
S2E18 "Up the Long Ladder"
S2E19 "Manhunt"
S2E21 "Peak Performance"
S2E22 "Shades of Gray"
S3E5 "The Bonding"
S3E6 "Booby Trap"
S3E9 "The Vengeance Factor"
S3E11 "The Hunted"
S3E12 "The High Ground"
S3E18 "Allegiance"
S3E19 "Captain's Holiday"
S3E20 "Tin Man"
S3E24 "Menage a Troi"
S3E25 "Transfigurations"
S4E4 "Suddenly Human"
S4E8 "Future Imperfect"
S4E10 "The Loss"
S4E13 "Devil's Due"
S4E14 "Clues"
S4E16 "Galaxy's Child"
S4E17 "Night Terrors"
S4E18 "Identity Crisis"
S4E19 "The Nth Degree"
S4E20 "Qpid"
S4E22 "Half a Life"
S4E23 "The Host"
S5E6 "The Game"
S5E9 "A Matter of Time"
S5E11 "Hero worship"
S5E12 "Violations"
S5E13 "The Masterpiece Society"
S5E17 "The Outcast"
S5E20 "Cost of Living"
S5E22 "Imaginary Friend"
S6E2 "Realm of Fear"
S6E3 "Man of the People"
S6E5 "Schisms"
S6E6 "True Q"
S6E7 "Rascals"
S6E9 "The Quality of Life"
S6E13 "Aquiel"
S6E22 "Suspicions"
S6E23 "Rightful Heir"
S6E26 "Descent Part 1"
S7E1 "Descent Part 2"
S7E2 "Liaisons"
S7E3 "Interface"
S7E6 "Phantasms"
S7E7 "Dark Page"
S7E9 "Force of Nature"
S7E10 "Inheritance"
S7E13 "Homeward"
S7E14 "Sub Rosa"
S7E17 "Masks"
S7E18 "Eye of the Beholder"
S7E19 "Genesis"
S7E22 "Bloodlines"
S7E23 "Emergence"
Deep Space Nine:
S1E5 "Babel"
S1E7 "Q Less"
S1E9 "The Passenger"
S1E10 "Move Along Home"
S1E14 "The Storyteller"
S1E16 "If Wishes Were Horses"
S1E17 "The Forsaken"
S2E6 "Melora"
S2E7 "The Rules of Acquisition"
S2E9 "Second Sight"
S2E10 "Sanctuary"
S2E11 "Rivals"
S2E17 "Playing God"
S2E18 "Profit and Loss"
S3E4 "Equilibrium"
S3E7 "Civil Defense"
S3E8 "Meridian"
S3E10 "Fascination"
S3E16 "Prophet Motive"
S3E18 "Distant Voices"
S3E25 "Facets"
S4E10 "Our Man Bashir"
S4E21 "The Muse"
S5E6 "Trials and Tribble-ations"
S5E7 "Let He Who Is Without Sin..."
S5E8 "Things Past"
S5E17 "A Simple Investigation"
S5E20 "Ferengi Love Songs"
S6E8 "Resurrection"
S6E10 "The Magnificent Ferengi"
S6E21 "The Reckoning"
S6E22 "Valiant"
S6E23 "Profit and Lace"
S6E24 "Time's Orphan"
S6E25 "The Sound of her Voice"
S7E5 "Chrysalis"
S7E12 "The Emperor's New Cloak"
S7E13 "Field of Fire"
S7E14 "Chimera"
Voyager:
S1E8 "Ex Post Facto"
S1E9 "Emanations"
S2E1 "The 37s"
S2E4 "Elogium"
S2E5 "Non Sequitur"
S2E6 "Twisted"
S2E9 "Tattoo"
S2E15 "Threshold"
S2E22 "Innocence"
S3E5 "False Profits"
S3E7 "Sacred Ground"
S3E11 "The Q and the Grey"
S3E12 "Macrocosm"
S3E15 "Coda"
S3E19 "Rise"
S3E20 "Favorite Son"
S3E25 "Displaced"
S4E17 "Retrospect"
S4E20 "Vis a Vis"
S4E22 "Unforgettable"
S4E24 "Demon"
S5E4 "In The Flesh"
S5E12 "Bride of Chaotica"
S5E13 "Gravity"
S5E17 "The disease"
S5E18 "Course: Oblivion"
S5E19 "The Fight"
S5E23 "11:59"
S6E02 "Survival Instinct"
S6E18 "Ashes to Ashes"
S6E21 "Live Fast and Prosper"
S6E23 "Fury"
S6E25 "The Haunting of Deck 12"
S6E26 "Unimatrix Zero" (Watch the scene at the beginning on the bridge but that's it)
S7E1 "Unimatrix Zero"
Swap the order of "Drive" and "Imperfections"
S7E4 "Repression"
S7E6 "Inside Man"
S7E8 "Nightingale"
S7E11 "Shattered"
S7E14 "Prophecy"
S7E19 "Q2"
S7E21 "Friendship One"
S7E22 "Natural Law"
S7E24 "Renaissance Man"
Movies:
Star Trek V: The Final Frontier
Star Trek: Generations
Star Trek: Insurrection
Star Trek: Nemesis
Star Trek 2009
Retcon - Star Trek: First Contact takes place some time between 50485.2 and 50537.2, not 50893.5
Star Trek: First Contact takes place between the DS9 S5 episodes "For the Uniform" and "In Purgatory's Shadow"
Star Trek: First Contact takes place between the Voyager S3 episodes "Alter Ego" and "Blood Fever"