Although I am a grad student in the physical sciences, I can't program at all, so until I figure out how to make more modules look like the Favorites ones, you're getting lists here.

Favorite Serieses:
Nuptialverse by Darth Link 22
"Post-Nuptials"
"Families"

To Love Trilogy by Brony2893
"To Love a Goddess"
"To Love a Mortal"

Farringtonverse by Nicknack
"Heart of Gold, Feathers of Steel"
"Summer Days"
"Evening Flames"
(Telling the story of Gilda and the fallout from "Griffon the Brush Off" ranging from her motivations before that episode through her new job as a city guard of Farrington, a city near the Griffon/Equestria border. Gilda has been banished from her tribe and even from seeing another griffin, under penalty of death, unless she completes a quest to kill Rainbow Dash. She won't kill her friend, but coming into Ponyville to explain her situation gets her nowhere except on the wrong side of the Mane 6. Returning injured and in disgrace to the nearest city to her cave/home, she finds a kind-hearted Captain of the Guard who offers her a job in the Guard. In the relatively anti-griffin city, Gilda struggles to find her place amongst hostile crime lords, furious guards, and ponies who truly care for her. The flow from one character's POV to another in the narrative is incredibly well done as is the description of the setting.)
((Also, fanboy squee that my invented term for this series caught the eye of the author himself. ))

Cadance of Cloudsdale Cycle by Skywriter
"How to Remove a Unicorn Tooth"
"Cadance of Cloudsdale"

Arcanus E Draconus series by InsertAuthorHere
"My Little Alicorn"
"Bringing Up Blueblood"
"Waning Moon"

Blueblood's Destiny series (my name) by Kavonde
"A Teacher with No Class"
"The Strange Destiny of Prince Blueblood"
"The Prince of Ponyville"
(I must admit that I'm somewhat disappointed that half of the final chapter is the outline for the rest of the story as opposed to the actual rest of the story, but I'll take what I can get since I quite enjoy Blueblood stories.)

Derring-Doo Duology (my name)
"Biased and Incomplete"
"The Death of Daring Do: The Engine of Eternity"

The Equestrian Civil Service series (my name)
"Whom the Princesses Would Destroy..."
"A Canterlot Carol"
(Why, you ask? It's Canterlot Slice of Life, focused on civil servants, trying to allay concerns like: "Every time Twilight Sparkle was scheduled to meet with the princess, he had to reassure pretty much every ambassador, legate, consul, and special envoy, often personally, that Equestria wasn't going to invade anypony just yet.")

Aegis Shield's Lunar Stallionverse (my name)
Luna's Story: Rise of the Lunar Stallions
Let the Silence Sing
Luna's Story 2: Wrath of the Moon Champion
Luna's Story 3: Long Live the Night
Twilight and the Spartan Stallion
(Luna's Stories take place somewhat contemporaneously with Let the Silence Sing (which was the first story I read on this site). With Luna's return from exile, she resurrects an ancient order of Royal Guards starting with two former Guards. Characters carry over between stories so my headcanon says that they are in the same universe.)

The Return of Princess Nightmare Moon
The Affection of Princess Nightmare Moon
(Princess Luna never existed, instead Celestia's coruling sister was always Nightmare Moon: a night goddess of wine, fertility, and lust. Returning home from here Lunar exile, she immediately collapses from her weakness and is rushed to a hospital where she is slowly nursed back to health. Her physical therapist, Bandaid, intrigues her so much so that she demands that he become her personal nurse during her out-patient recovery. When Chrysalis comes to renew an old fling, Nightmare Moon, Bandaid, and Celestia discover, to their horror, the cause of the madness 1000 years ago. Meanwhile, Prince Blueblood seeks to court Twilight Sparkle, the recently appointed Vizier, and two twin lunar guards fall in love with two twin changeling guards and elope.)

Seeing the Pattern
Seeing the Pattern 2: Death Take You