These are the ones I Have rated as 5/5 on the guide:
The Holy Terror
The Chimes of Midnight
Creatures of Beauty
The Natural History of Fear
Home Truths
The Magic Mousetrap
Ringpullworld
The Architects of History
The Guardian of the Solar System
Deimos/The Ressurection of Mars
A Death in the Family
Rise and Fall
Farewell, Great Macedon
The Cold Equations
The Rocket Men
The Elite
The Curious Incident of the Doctor in the Night Time
Fall to Earth
Broken
A Full Life
How to Win Planets and Influence People
The Sky Man
We Always Get Out Alive
The Master of Callous
Ghost Station
Parasite: The Dead Hand
Expiry Dating
The Trojan Dalek
Friend of the Family
Broken Hearts.
Looking back, I’d probably drop a few of those to a 4.5, and I’m sure there’s some stories that missed out that I might move up to a 5 at some point, but it’s a pretty good list I think.
These are the favorites from my current super chronological run-through (note, I’m just about to finish up Two in the next few weeks so there’s very much a black and white focus):
In addition to those, the absolutely incredible Diary of River Song: Friend of the Family is one of the greatest pieces of any Doctor Who related media ever:
And off the top of my head beyond those just skimming through my app:
I’ll second pretty much everything by Rob Shearman (aside from the obvious)
The Church and the Crown
The Main Range Villains Trilogy (Omega, Davros, and Master)
The Arrangements For War/Thicker Than Water duo
Pretty much almost anything from the original Hex arc but shoutouts to The Harvest, Live 34, The Settling, A Death in the Family, and Protect and Survive
The 1963/50th Anniversary Main Range Trilogy (Fanfare for the Common Men, The Space Race, and The Assassination Games)
The Five/Nyssa/Tegan/Marc storyline (Tartarus - Nightmare of the Daleks)
Lepidoptery for Beginners
Solitaire
The Elite
The Foe From the Future
Wrath of the Iceni
UNIT Dominion
The Last Post
The Auntie Matter
Anything involving The Scorchies (I’m begging BF to bring these guys back to fight Ol Sixie)
The Crooked Man
The Fifth Doctor Box Set (Psychodrome and Iterations of I)
The entire Philip Hinchcliffe Presents series
The Triumph of Sutekh
The Paradox Planet/Legacy of Death
Death and the Queen
The Trouble With Drax
Skin of the Sleek/The Thief Who Stole Time
The Diary of River Song Volume 3
The Third Doctor Adventures Volume 4
The Fourth Doctor Adventures Series 7
Better Watch Out/Fairytale of Salzburg
I Am the Master
The Master of Callous
Companion Piece
Torchwood: The Story Continues
Nightmare Country
The War Master: Anti-Genesis
The Fourth Doctor Adventures Series 9
R & J
The Tenth Doctor & River Song
Dalek Universe
Girl, Deconstructed
The Diary of RIver Song: New Recruit
Monsters in Metropolis
Peladon
Auld Lang Syne
Together in Electric Dreams
The Auton Infinity
The New Adventures of Bernice Summerfield: Blood and Steel
You know, I seem to vaguely remember thinking highly of The Chimes of Midnight. So many people are citing it here that - when I get through the discs I actually own - that may be the first unowned story I hunt down for a re-listen.