Story arc

Listed below are various story arcs that have featured within Doctor Who canon, in order of story, season or series production which then lists the story arc present throughout those stories, season or series.

Doctor Who
Doctor Who television stories Classic Revival
 * Season 8 - The Master arc
 * Season 16 - The Key to Time
 * Season 18 - Journey in E-Space
 * Season 18/Season 19 - The Return of the Master/ New Beginnings
 * Season 20 - The Black Guardian
 * Season 23 - The Trial of a Time Lord
 * Series 1 - The Bad Wolf meme
 * Series 2 - The Torchwood Institute
 * Series 3 - Harold Saxon
 * Series 4 - The Shadow Proclamation, the Medusa Cascade, Disappearing Bees, Lost Worlds, The Return of Rose, Prophecies and the Bad Wolf meme
 * 2009 Specials - Tenth Doctor's Regeneration
 * Series 5 - Cracks in Time, The Silence

Virgin New Adventures

 * Timewyrm: Genesys, Timewyrm: Exodus, Timewyrm: Apocalypse, Timewyrm: Revelation - Timewyrm arc
 * Cat's Cradle: Time's Crucible, Cat's Cradle: Warhead, Cat's Cradle: Witch Mark - Cat's Cradle arc
 * Blood Heat, The Dimension Riders, The Left-Handed Hummingbird, Conundrum and No Future - Alternate Universe arc

BBC Eighth Doctor Adventures

 * Alien Bodies, Unnatural History, Interference - Book One, Interference - Book Two, The Taking of Planet 5, The Shadows of Avalon, The Ancestor Cell - Time Lords' future war with The Enemy
 * The Ancestor Cell, The Burning, Casualties of War, The Turing Test, Endgame,Father Time, Escape Velocity - Lost memory and second exile in Earth.

The New Eighth Doctor Adventures

 * Blood of the Daleks, human Resources, Grand Theft Cosmos, Worldwide Web - Headhunter saga
 * Situation Vacant, Nevermore The Book of Kells, The Resurrection of Mars, Lucie Miller, To the Death - The revenge of the Time Meddler.

Virgin Bernice Summerfield New Adventures

 * Where Angels Fear, The Mary-Sue Extrusion, Dead Romance, Return to the Fractured Planet, Twilight of the Gods - Dellahan gods arc

Torchwood
Torchwood television stories
 * Series 2 - The Resurrection of Owen Harper - Reset, Dead Man Walking & A Day in the Death

Trilogies
Similar to the "Story Arcs" but consisting of 3 stories, some in books, some in episodes and others in "Audio Play."

In books

 * MA: Cold Fusion, NA: The Death of Art, NA: Sleepy: Psi Powers arc
 * MA: The Scales of Injustice, PDA: Business Unusual, PDA: Instruments of Darkness: Pale Man and Irish Twins Trilogy

In audio play

 * The Reaping, The Gathering, The Harvest : Cybermen Trilogy.
 * The Key 2 Time - The Judgement of Isskar, The Key 2 Time - The Destroyer of Delights, The Key 2 Time - The Chaos Pool: the Key 2 Time Trology
 * Project: Twilight - Project: Lazarus - Project: Destiny:
 * City of Spires - The Wreck of the Titan - Legend of the Cybermen:

In TV series

 * New Earth, Gridlock, Last of the Time Lords: Face of Boe/Jack Harkness.
 * Resurrection of the Daleks,Revelation of the Daleks, Remembrance of the Daleks: The Dalek Civil War Trilogy