We know from Mulder and Frohike's conversation in "Emily" that Emily was not a unique creation. There are other children like her out there. These are their stories.

Children with an immediate biological connection to Scully and/or Mulder

An Act Of Kindness by Rotem Shahar
Alex II by laylya b.
All of The Children by Shiv
All or Nothing by trycee
All Which It Inherit 1: Insubstantial Pageant by Brandon D. Ray
All Which It Inherit 2: Melted Into Air by Brandon D. Ray
All Which It Inherit 3: Such Stuff As Dreams Are Made On by Brandon D. Ray
And I Rise by Leslie Sholly
...And So It Begins by Montana1416
Angerball by SnoopMar
Another by Dana Drives
Another by Dreamshaper
Another Child by Shoshana
Another One by Jodie
Arizona Highways by Fialka
Ashes Bitter on Her Tongue by Neoxphile

Baby Girl by Sara QueeQueg
Baby Mine by Debbie Gramlich
Bird in the Hand by Rachel Wilder
Bloodline I: Red by Cecily Sasserbaum
Bloodline II: Binding by Cecily Sasserbaum
Bringing Up Baby by Amber M Howard

Cassidy by Sara QueeQueg
The Children's Teeth universe by Erin McCole Cupp
Connections by Joeba
Crossroads in Time by Avalon

Darkness Ascending by Hillary
Daughter by Ducky's Dream
A Day In The Life by Goddess Michele
Daybreak 1. Dusk by Annie Jennings and Jennifer Frye
Daybreak 2. Night by Annie Jennings
Daybreak 3. Darkest Hour by Annie Jennings
Deceive, Inveigle, Obfuscate by Donnilee
Disquisitiones Arithmeticae: Projection by Eve11
Distance Covered by Naina

Eden's Reprise II (wip) by Deslea R Judd
Embers by Jamie Taylor
Emily Returns by Jessica Hildbold
The Emilys by Rocketman
Equinox by Mystic
The Eric series by Spookyteacher

The Family by Sandra W.
Fighting The Future by Kathleen Brown
Five Years and One Night by Shalimar
Fugue for the Forgotten by Crash and frogdoggie

A Gauntlet and a Gift by Leslie Sholly
Genesis by Ally
Ghostly Lullabies Tara W.
Great Men Universe: The Beginning by The Phile Formerly Known as Soapie
Great Men Universe: part one by The Phile Formerly Known as Soapie

The Hard Edges of Things by Neoxphile
the Help Me series by Ophelia K
Home For the Holidays by Neoxphile

I Shall Believe by Cathey Scully
I Should Have Known by ElleThom
I Want To Believe by Samantha
I Want To Believe II: Trying by Samantha
I Want To Believe III by Samantha
In AEternum by Diana NO Fowley
The Iolokus series by MustangSally and Rivka T
Iunctio ut Redimio - Book 1 by Kay
Iunctio ut Redimio - Book 2 by Kay

Jessica by Allison Potty
Jessica by Mystic

Katie by Danielle D

Leaders of the Colonies by Mystic
Letting Go by PhileyX
Liquid Memory by Sandra Stringer
Liquid Memory II: Benefit of the Doubt by Sandra Stringer
Little Fox by Empress Vader

The Miracle Before Christmas by Teliko. x3

Never Meant to Be by Tara Avery
Nine Hours by RogueAngel
Now I Lay Me Down To Sleep by Alanna

Offspring and Lives Incomplete by Donna
The Offspring by Kelli Rocherolle
Origins by Mischa
The Other Two by Taryn Crow

Pieced Together by Rachel Wilder
Portrait of a Family by Lilith
Progeny by Zephathah
Promise with Your Heart by Kathy Williams

Rachel by E. A.
Rainbow Continuum by Emily Miller
Re Vivus Facere by aka "Jake"
The Retrieval series by Daydreamer
The Rift and the Abyss by founta

Samuel and Come Get Me by Invisigoth421
Scully's Children by DanaFuchs
Secrets of the Gemini by Jei
Small Hostage by Anne Haynes
Sponsalia by The Jedi Shipper
The Spy in the Campaign by Dana'sFairytales
Stolen Promises by Mulderslady

Telephone by Agent Chloe
Tiuwak by Ccile Laumonier
Truckin' by Donnilee and FatCat
Truckin' II: Keep On Truckin' by Donnilee and FatCat
The Truth Is Out There And It Hurts by Dana'sFairytales

Verity by The Consortium

When The Bough Breaks by Jennifer L. Frye
A Winter's Tale by Anjou
Who Knew? by ElleThom
Wrapped in Wind by Rocketman

Lab created, but not Scully or Mulder's offspring
though some still are blood relatives of another kind:

Beyond The Truth series by Neoxphile
Consolation by Neoxphile
The Family G-Man by FelineFemme and Neoxphile
The Family G-Man: One Fine Summer by FelineFemme and Neoxphile
The Family G-Man: Confessions and Connections by Neoxphile and FelineFemme
The Family G-Man: IWTB by Neoxphile and Felinefemme
The Family G-Man: From Here to Paternity by Neoxphile and Felinefemme
Frederick by Lillydale
Genesis project by aRcaDIaNFall$
Her Brother, Fox by TCS1121
In Death, there is Life by Josan
Star by Bardsmaid
Things Bright and Green by DBKate

More stories fitting these two themes:

at Gossamer
Dark Emerald by Cassie & Shanda Weeks (unfinished)
Return to The Nursery Files