The TV Whoniverse
Doctor Who 1963-89
Lesley Scott - The Ark (1966) with Paul Erickson - though received wisdom is that she did not in fact write any of it.
Barbara Clegg - Enlightenment (1983) - one of two sole and undisputed credits for women writers in Old Who
Paula Moore - Attack of the Cybermen (1985) - extent of Moore's authorship hotly disputed (her real name is Paula Woolsey).
Jane Baker - The Mark of the Rani (1985), Terror of the Vervoids (1986), The Ultimate Foe Episode 14 only (1986), Time and the Rani (1987) all with Pip Baker
Rona Munro - Survival (1989) - the second sole and undisputed credit for a women writer in Old Who
Doctor Who 2005-
Helen Raynor - Daleks of Manhattan/Evolution of the Daleks (2007), The Sontaran Stratagem/The Poison Sky (2008).
Sarah Jane Adventures
No credited women writers.
Torchwood
Helen Raynor - Ghost Machine (2006), To The Last Man (2008)
Jacquetta May - Random Shoes (2006)
Catherine Tregenna - Out of Time (2006), Captain Jack Harkness (2007), Meat (2008), Adam (2008)
Doris Egan - Miracle Day: Rendition (2011)
Jane Espenson - Miracle Day: Dead of Night, The Categories of Life, Immortal Sins, (with Ryan Scott) End of the Road, (with Russell T. Davies) The Blood Line (all 2011)
K9
Deborah Parsons - The Sirens of Ceres, Oroborus and The Lost Library of Ukko (all 2009)
TV Spinoffs
The girls of Oakley Junior School - Death is the Only Answer (2011), with the boys of Oakley Junior School.
Jane Espenson - Torchwood: Web of Lies (2011) - animated story
Books
Target Novelisations
Barbara Clegg - Doctor Who: Enlightenment (1984)
Jane Baker - Doctor Who: The Mark of the Rani (1986), Doctor Who: Terror of the Vervoids (1988), Doctor Who: Time and the Rani (1988), Doctor Who: The Ultimate Foe (1988) all with Pip Baker
Alison Bingemann - Doctor Who: The Celestial Toymaker (1986) - credited as co-writer with Gerry Davis though in this case the lore is that Bingemann did most of the writing
Rona Munro - Doctor Who: Survival (1990)
Virgin New Adventures
Kate Orman - The Left-Handed Hummingbird (1993), Set Piece (1995), SLEEPY (1996), Return of the Living Dad (1996), The Room With No Doors (1997), So Vile A Sin (1997) - last of these co-written with Ben Aaronovitch
Virgin Missing Adventures
None
Eighth Doctor Adventures
Kate Orman - Vampire Science (1997), Seeing I (1998), Unnatural History (1999), The Year of Intelligent Tigers (2001) - first three of these co-written with Jonathan Blum
Natalie Dallaire - Parallel 59 (2000) with Stephen Cole
Jacqueline Rayner - EarthWorld (2001)
Lloyd Rose - The City of the Dead (2001), Camera Obscura (2002)
Kelly Hale - Grimm Reality (2002) with Simon Bucher-Jones
Mags L Halliday - History 101 (2002)
Past Doctor Adventures
Kate Orman - Blue Box (2003)
Jacqueline Rayner - Wolfsbane (2003)
Lloyd Rose - The Algebra of Ice (2004)
New Series Adventures
Jacqueline Rayner - Winner Takes All (2005), The Stone Rose (2006), The Last Dodo (2007), The Sontaran Games (2009), The Darksmith Legacy: The Picture of Emptiness (2009), Magic of the Angels (2012), The Water Thief (2012)
Una McCormack - The King's Dragon (2010), The Way Through the Woods (2011)
Naomi Alderman - Borrowed Time (2011)
J.T. Colgan (better known as chick-lit author Jenny Colgan) - Dark Horizons (due later 2012)
Telos novellas
Louise Cooper - Rip Tide (2003)
Kate Orman - Fallen Gods (2003) with Jonathan Blum
Bernice Summerfield novels
Kate Orman - Walking to Babylon (1998)
Rebecca Levene - Where Angels Fear (1998) with Simon Winstone
Jacqueline Rayner - The Squire's Crystal (2001), The Glass Prison (2001)
Xanna Eve Chown - Legion (coming in 2012)
Torchwood novels
Sarah Pinborough - Into the Silence (2009), Long Time Dead (2011)
Faction Paradox novels
Mags L. Halliday - Warring States (2005)
Kelly Hale - Erasing Sherlock (2006)
Erimem novel
Claire Bartlett - The Coming of the Queen (2005) with Iain McLaughlin
Short stories
Karen Dunn - "An Unfulfilled Dream" (in DWM 178, 1991)
Kate Orman - "The Useful Pile" (in DWM 188, 1992); "One Minute Fourteen Seconds" (in DWM 206, 1993); "No Exit" (in Short Trips: Steel Skies, 2003); "The Southwell Park Mermaid" (in Short Trips: Life Science, 2004); "Culture War" (in Short Trips: 2040, 2004); "Nobody's Gift" (in Short Trips: The History of Christmas, 2005); "White on White" (in Short Trips: Christmas Around The World, 2008)
Vanessa Bishop - "A Visit to the Cinema" (in DWM 190, 1992); "Playtime" (in 1992 DWM Holiday Special); "The Straw That Broke The Camel's Back" (in Decalog, 1994); "Time Share" (in Decalog 2: Lost Property, 1995); "The Feast of Seven... Eight (and Nine)" (in Short Trips: A Christmas Treasury, 2004)
Una McCormack - "A Time & a Place" aka "Time and Time Again" (in DWM 197, 1993); "The Slave War" (in Short Trips: The Quality of Leadership, 2008)
Pam Baddeley - "People of the Trees" (in Decalog 2: Lost Property, 1995)
Jackie Marshall - "Past Reckoning" (in Decalog 3: Consequences, 1996); "Lily" (in Short Trips: A Christmas Treasury, 2004)
Rebecca Levene - "The Last Days" (as Evan Pritchard in Short Trips, 1998); "Cold War" (in Short Trips: Steel Skies, 2003); "Anteus" (in Short Trips: 2040, 2004); "Too Rich for My Blood" (in Short Trips: Seven Deadly Sins, 2005); "No Room" (in Short Trips: Christmas Around The World, 2008)
?Sam Lester - "There Are Fairies At The Bottom Of The Garden" (in Short Trips, 1998)
Harriet Green - "Planet of the Bunnoids" (in Short Trips and Side Steps, 2000)
Sarah Groenewegen - "Virgin Lands" (in Short Trips: Zodiac, 2002); "Hymn of the City" (in Short Trips: The Muses, 2003); "The Bushranger's Story" (in Short Trips: Repercussions, 2004)
Alison Lawson - "The Stabber" (in Short Trips: Zodiac, 2002); "A Long Night" (in Short Trips: Companions, 2003); "Far from Home" (in Short Trips: Past Tense, 2004); "Saturn" (in Short Trips: The Solar System, 2005)
Juliet E. McKenna - "Losing Track of Time" (in Short Trips: A Universe of Terrors, 2003)
Claire Bartlett - "Graham Dilley Saves the World" (with Iain McLaughlin, in Short Trips: Past Tense, 2004); "The Time Lord's Story" (with Iain McLaughlin, in Short Trips: Repercussions, 2004)
Kathryn Sullivan - "The Diplomat's Story" (in Short Trips: Repercussions, 2004)
Samantha Baker - "Fixing A Hole" (in Short Trips: Past Tense, 2004); "These Things Take Time" (in Short Trips: Monsters, 2004); "Be Good For Goodness's Sake" (in Short Trips: The History of Christmas, 2005); "Childhood Living" (in Short Trips: The Centenarian, 2005)
Jacqueline Rayner - "Screamager" (in Short Trips: Monsters, 2004); "The Last Emperor" (in Short Trips: 2040, 2004); linking material (in Short Trips: Seven Deadly Sins, 2005)
Xanna Eve Chown - "Daisy Chain" (in Short Trips: 2040, 2004); "A Life in the Day" (in Short Trips: A Day in the Life, 2005); "Saint Nicholas's Bones" (in Short Trips: The History of Christmas, 2005); "Do You Believe in the Krampus?" (in Short Trips: The Ghosts of Christmas, 2007); "One Card For The Curious" (in Short Trips: Defining Patterns, 2008)
?Val Douglas - "In the TARDIS: Christmas Day" (in Short Trips: A Christmas Treasury, 2004)
Karen Dunn - "UNIT Christmas Parties: Ships That Pass" (in Short Trips: A Christmas Treasury, 2004)
Alison Jacobs - "One Wednesday Afternoon" (in Short Trips: A Day in the Life, 2005)
Lizzie Hopley - "First Born" (in Short Trips: The Centenarian, 2005)' "Golem" (in Short Trips: Snapshots, 2007); "Stanley" (in Short Trips: Defining Patterns, 2008)
Mary Robinette Kowal - "Suspension and Disbelief" (in Short Trips: Destination Prague, 2007)
Lucy A. Snyder - "Fable Fusion" (with Gary A. Braunbeck, in Short Trips: Destination Prague, 2007)
Helen Raynor - "All of Beyond" (in Short Trips: Snapshots, 2007)
Ann Kelly - "The Cutty Wren" (in Short Trips: The Ghosts of Christmas, 2007)
Diane Duane - "Goths and Robbers" (in Short Trips: The Quality of Leadership, 2008)
Terri Osborne - "Good Queen, Bad Queen, I Queen, You Queen" (in Short Trips: The Quality of Leadership, 2008)
Linnea Dodson - "God Send Me Well to Keep" (in Short Trips: The Quality of Leadership, 2008)
Kathleen O. David - "On a Pedestal" (in Short Trips: The Quality of Leadership, 2008)
Mags L. Halliday - "Gudok" (in Short Trips: Transmissions, 2008)
Kelly Hale - "Nettles" (in Short Trips: Transmissions, 2008)
L.M. Myles - "Child's Play" (in Short Trips: How The Doctor Changed My Life, 2008)
Violet Addison - "Those Left Behind" (in Short Trips: How The Doctor Changed My Life, 2008)
Anna Bratton - "Lares Domestici" (in Short Trips: How The Doctor Changed My Life, 2008)
Lisa Miles - "A Visit from Saint Nicholas" (in Short Trips: Christmas Around The World, 2008)
?J.J. Secker - "The Doctor's Cross Word" (in Short Trips: Christmas Around The World, 2008)
Beverley Allen - Autaia Pipipi Pia (in Short Trips: Christmas Around The World, 2008)
Spinoff short stories
Kate Orman - "No One Goes to Halfway There" (in Decalog 4: Re-Generations, 1997); "Steal From the World" (in Bernice Summerfield collection The Dead Men Diaries, 2000); "Solar Max and the Seven-Handed Snake-Mother" (in Bernice Summerfield collection A Life of Surprises, 2002); "The Peter Principle" (in Bernice Summerfield collection Life During Wartime, 2003); "Buried Alive" (in Bernice Summerfield collection A Life Worth Living, 2004); "Lock" (in Bernice Summerfield collection Collected Works, 2006); "All Mimsy Were the Borogoves" (in Bernice Summerfield collection Nobody's Children, 2007); "Don't Do Something, Just Sit There" (in Bernice Summerfield collection Present Danger, 2010)
Liz Holliday - "Burning Bright" (in Decalog 4: Re-Generations, 1997)
Caroline Symcox - "A Question of Identity" (in Bernice Summerfield collection The Dead Men Diaries, 2000)
Kathryn Sullivan - "The Monster and the Archaeologist" (in Bernice Summerfield collection The Dead Men Diaries, 2000)
Mags L. Halliday - contributor to Faction Paradox The Book of the War (2002); "Cabinets of Curiosities" (in Bernice Summerfield collection Collected Works, 2006); "The Badblood Diaries" (in Bernice Summerfield collection The Vampire Curse, 2008)
Kelly Hale - contributor to Faction Paradox The Book of the War (2002); "Possum Kingdom" (in Bernice Summerfield collection The Vampire Curse, 2008); "The Little Bighorn Casino" (in Iris Wildthyme collection Iris: Abroad, 2010)
Helen Fayle - contributor to Faction Paradox The Book of the War (2002);
Lloyd Rose - "Afterword" (in Bernice Summerfield collection A Life of Surprises, 2002)
Jo Fletcher - "On Being Five" (in Short Trips: A Christmas Treasury, 2004)
Rebecca Levene - "The Serpent's Tooth" (in Bernice Summerfield collection Parallel Lives, 2006)
Sharon Gosling - "Alby" and "Suz" (in Short Trips: Dalek Empire, 2006)
Xanna Eve Chown - "Biology Lesson on Mal Oreille" (in Bernice Summerfield collection Missing Adventures, 2007)
Sarah Pinborough - "Kaleidoscope" (in Torchwood collection Consequences, 2009)
Jac Rayner and Orna Petit - "The Niceness" (in Iris Wildthyme collection The Panda Book of Horror, 2009)
Liz Myles - "The Better Part of Valour" (in Bernice Summerfield collection Present Danger, 2010)
Violet Harrison - "Nothing Lasts Forever" (in Faction Paradox collection A Romance in Twelve Parts, 2011) with David N. Smith
Audios
Big Finish main sequence
Jacqueline Rayner - The Marian Conspiracy (2000); Doctor Who and the Pirates (2003); "100 BC" (in 100, 2007); The Doomwood Curse (2008)
Caroline Symcox - Seasons of Fear (2002) with Paul Cornell; The Council of Nicaea (2005)
Lloyd Rose - Caerdroia (2004)
Alison Lawson - Catch-1782 (2005)
Catherine Harvey - "Recorded Time" (in Recorded Time and Other Stories, 2011)
Emma Beeby - The Doomsday Quatrain (2011) with Gordon Rennie
Lost Stories
Barbara Clegg - Point of Entry (2010) with Marc Platt; The Elite (2011) with John Dorney
Ingrid Pitt - The Macros (2010) with Tony Rudlin
Hazel Adair - Hexagora (2011) with Peter Ling and Paul Finch
BF special release
Claire Bartlett - The Veiled Leopard (2006) with Iain McLaughlin
Companion Chronicles
Jacqueline Rayner - Transit of Venus (2009); The Suffering (2010)
Short Trips
Ally Kennen - "The Deep" (in Short Trips Vol 1, 2010)
Dorothy Koomson - "Running Out Of Time" (in Short Trips Vol 1, 2010)
Sharon Cobb - "Sock Pig" (in Short Trips Vol 2, 2011) with Iain Keiller
Kate Orman - "The Five Dimensional Man" (in Short Trips Vol 3, 2011)
Juliet Boyd - "The Wondrous Box" (in Short Trips Vol 3, 2011)
Mathilde Madden - "Wet Walls" (in Short Trips Vol 3, 2011)
Cindy Garland - "To Cut A Blade Of Grass" (in Short Trips Vol 4, 2011)
Avril Naude - "Quantum Heresy" (in Short Trips Vol 4, 2011)
Spinoffs
Jacqueline Rayner - adapted four novels, including Kate Orman's Walking to Babylon, for the first season of Bernice Summerfield audios in 1998-2000 and is adapting Paul Cornell's Love and War for release in 2012; also wrote The Grel Escape (2004), The Kingdom of the Blind (2005), Buried Treasures (2010) with Paul Cornell, and Epoch: The Temple of Questions (2011)
Fiona Moore - the Kaldor City stories Hidden Persuaders (2002) with Jim Smith, and The Prisoner (2004) with Alan Stevens
Claire Bartlett - UNIT: Time Heals (2004) and UNIT: The Wasting (2005), both with Iain McLaughlin
Comics
Karen Dunn - "Cambridge Previsited" (in Doctor Who Yearbook 1993)
Kate Orman - "Change of Mind" (in DWM 221-223, 1995)
Jacqueline Rayner - "Mirror Image" (in DWA 2, 2006)
Claire Lister - "Plague Panic" (in Battles in Time 16, 2007); "Exhausting Evil" (in Battles in Time 17, 2007); "Minor Trouble" / "Inhuman Sacrifice" / "Crimes and Punishment" (in Battles in Time 31-33, 2007)
Leah Moore - The Whispering Gallery (IDW, 2009) with John Reppion
Carole E. Barrowman - "The Selkie - A Captain Jack Tale" (in Torchwood Magazine 14, 2010) with John Barrowman
I am sure that this list has many mistakes; please tell me my omissions and errors in comments.
Edited to add: Thanks to commenters for pointers on Faction Paradox, JR Loflin, JAckie MArshall and LM Myles.