Any fics that are marked +E contain canon Emily as well as the post-Requiem baby

Girls

About Daddy by Heather Riggall(Samantha)

Ad Astra per Aspera by Charlotte Unsworth (Meghan)

Ad Vitam Aeternam by Foxsong

An Advanced Case of Like by C and Me (Shannon)

Amanda series by Mary Kleinsmith

And I Drove Away by Becka F.

Baby Girl Window by Becka F.

Bittersweet Renaissance by Caroline

Breath In, Breath Out by little Starbuck*

Butterfly Kiss by Diana Rubenstein (Eva)

the Changed series by Cathey Scully (Akila and Gina)

China Roses by Knex Wildfire (Elizabeth)

Cleaning My Room by Rhiannon R (Samantha)

Closer by BioGirl (Gena)

Coin by IAmSam (Sammi)

Come Back To Me by Renee Delrigo (Hope)

Dancing in the Rain by DC Luder

Delivery at the Corner of Dupont and Connecticut by Rachel Wilder

Die Anworten by Opal

Dream Energy by xfilesqueen

A Dream of Thaw by M. Sebasky (Sarah)

Exit by Alcott

Faith by DKNYScully

First Born by diamondlife17 (Grace)

Fringe Series by Michelle Kiefer (Kate)

Glass Landscape by Annie Sewell-Jennings (Bess)

The Ground Floor by Meliss

Hem Ben Ik by Livia Balaban (Erin)

Home to Stay by Muldersangel (Kristen) +E

I Love You, Goodbye by Dana Katherine Scully (Samantha)

In My Last Moments by Ara (Crevan)

Later by Diadem

The Man to His Left by Jeri (Anna)

Maria de los Dolores by Mindy J

Maria de los Dolores II by Mindy J

Maya I-III by Diana R.

Me, Sam by Hardra61

Me, Sam II by Hardra61

The Measure of My Days by Marguerite (Ruth)

Mulder, It's Time! by Mulderache (Maddie)

Never Coming Back/Never Going to Go Away by Julia DH (Katie)

No Room For Tears by Hardra61 (Sam)

Nova by Angel (Aeryn)

Now Is the Time by Anndie (Sami)

On Angels from Heaven by Sandee (Angel)

Papa's Got a Brand New Bag by Kel (Katherine Claire)

Pregnant Mulder by Bertie (Jenny)

Rainy Rendezvous by Lonegunwoman (Samantha)

Requited Reverie by Kailee W (Hannah)

Rescue Mission series by Laura Means (Grace)

The Return by Katriena Knights (Alexis)

Return to Me by Allison B (Samantha)

Reunion by Jenna Tooms (Hannah)

Sacrificed Futures by Nerys (Mary)

Second Coming by RocketMan (Isabel)

Shoulders by Missy J (Uriana Scully)

Someone I Once Knew (Sara)

StarDust by Quinn Hegal (Angela Joanna aka Jo)

Stay With Me Always by Scully's Baby Blues (Brenna)

Survivors by lil gusty (Katie)

SUZ by AT (Suzanna)

Take My Breath Away by Ayla (Shayla)

To Breathe Again by Maddict (Haley)

Unspoken by Megan C (Hannah)

Where Day is Dark as Sleep (Veronica)

Where You Are by LoveFox42 (Maureen)

White Wave by Leyla Harrison (Hope)

Wish You Were Here by Brianne C (Samantha)

Wrapped in Memories by Rachel Freeman

X Is For Xenogenic by Donnilee

Xenophobia by Donnilee (Seena)

Yclept by RocketMan (Allie)

Boys

An Acceptable Level Of Happiness by Jenna Tooms (Malcolm)

Adopted Son by Kel (Stephen)

Another Gray Morning series by ML (David)

As Circumstances Allow by Ophelia (Walt)

Bed of Lies by Baby Blue1 (Nathan)

Bethlehem, Pennsylvania by Dramaphile

Birth by Teetee (Jacob)

Burning on Re-entry by bugs (Boy)

Christopher Ryan Scully series by Jori

Code Adam by Julie Cantrell (Joey)

Dark Seed by Bugs (Kit)

Deep Breath by Catherine M. (Samuel)

Duplicity by Archangel (David)

East Side of Eden by conspiracy (Nathan)

The Egg of the Phoenix by Keladry (Nicholas)

Everlasting Miracle by DScully141 (Dante)

Fantasty in X Major by Ophelia (Walt)

The Final Miracle by DS|DeathStryke (Noble)

Final Miracle II. If I Had Met You on Some Journey by DS|DeathStryke (Noble)

Final Miracle III. The Curious Wedding of George Hale by DS|DeathStryke (Noble)

Footprints in The Sand by T Bishop (Adam)

Goodbyes/Hellos series by Donna (Danny)

Homecoming by Vickie Moseley (Drew)

It's the Most Wonderful Time of the Year by Texas Rose (Michael)

Letonia by Cherry Ice (Evan)

Letonia II. The Ties That Bind by Cherry Ice (Evan)

Maggie's Tips for an Unforgettable Baby Shower by Kel and Scetti (Patrick)

My Father's Son by Elizabeth L. Iacono (Drew)

My Father's Eyes by Elizabeth L. Iacono (Drew)

My Father's Words by Elizabeth L. Iacono (Drew)

My Father's Stars by Lola Ravenhill/Elizabeth L. Iacono (Drew)

The Night We Never Met by Heidi P. (Johnny)

Progenesis by T Bishop (Adam)

Resist or Die by Cinnamon Scully (John)

Shattered Halcyon by Cinnamon Scully (John)

She Wishes I & II by Starbuck_Jayne (Matthew)

Shooting Star by Jenna Tooms (Ben)

Sieg Und Verlust aka "Jake" (John)

Silent Distances by C and Me (Sammy)

Ut Filium Suum Unigenitum by FredaX (John)

Vulpecula by Jeri (Adam)

With Arms Wide Open by Paige Caldwell (Matthew)

Without Fear by Michel (Michael)

A World to Save by geb (Gabe)

Multiple Babies

Fics marked +W have canon William in them as one of the children

"...and a Million Years Gone By" by DScully141 (Emma and Hope)

Counting Blessings by Diadem

Folded Like A Saint by kim1013 +W

Great Expectations by bellefleur and Emily Sims (Abigail and Amanda)

Joy Begets Sorrow by Parrotfish

Joyful are the Waterdrops by kim1013 +W

Nightmare series by aka "Jake" (Katherine & twin brother)

Origins by Mischa +W

The Present Implies Presence by kim1013 +W

The Present Implies Presence by kim1013 +W

Recovering Gemini by Neoxphile +W

The Truth is Out There by Lolabeegood +W

Sunday Goodbyes by kim1013 +W

Unknown Lives by Donna +W

Umm....

Five Twinkies, an Alien Baby, and Chris Carter by mysterygirl1

Having My Alien Baby by Alelou's Evil Twin

Lamb by LostInOblivion

Unknown Lives by Donna +W

Find more more kids and babies that aren't William or Emily on the Non-Canon Kids list