Lacuna, Brok the Investigator, Lamplight City, Misadventures of Laura Silver, Technobabylon, and Voodoo Detective.

I'd suggest Cognition: An Erica Reed Thriller, The Black Mirror, Circle of Blood

@ZapRowsdower I just added them, thank you for the suggestions!

@Penumbra Just added, thank you!

Suggestion, although a bit of an obscure pick: Animal Land Satsuijin Jiken/Animal Land Murder Case

@qbbyamiibo Just added! Thank you for the suggestion!

Amazing list for my favourite genre of fiction, just wanted to mention Roman's Christmas as I noticed it wasn't on the list!

Also the Ace Attorney Fangame: Gyaku Shaun Sai Hanri

@Zakdj thank you so much! Just added both games!

Wow, thanks for posting this list, it's incredibly thorough! I have some suggestions if you're looking for more.

Her Story has two follow-ups, Telling Lies and Immortality. Analogue: A Hate Story has a sequel, Hate Plus. Also 428: Shibuya Scramble (2008), Beyond (2005), Deadline (1982), Draugen (2019), Foo Foo (2016), Killed Until Dead (1986), Lunium (2023), Mizzurna Falls (1998), Moonmist (1986), and Murder on the Zinderneuf (1983).

Couple of other games that I've heard of but haven't played, but sound like they belong here? 2064: Read Only Memories, GameDec, Lux-Pain, Mask of the Rose, Scarlet Hollow, Shadows of Doubt, and Unavowed. Whew!

@bellwoods Thank you so much for so many suggestions!! 428: Shibuya Scramble and Unavowed were already on the list, but I just added the rest!

Wanted to leave some more obscure/newly added suggestions for the list:
Murders in Space
The Failure of Aniconfuku: Convention Murder Episode
The Crimson Debt
Murders on the Yangtze River
Wrongly Accused
We Suspect Foul Play
Eunae Liaro in: Fowl Play
Classified: of 2015
Murders at Tealwoods Manor
Clash: Robot Detective
Lucifer Within Us
Who Pressed Mute on Uncle Marcus?
Nina Aquila: Legal Eagle, Season One
Murder Mystery Machine
Oniria Crimes
Boodunnit
Sixtieth Kilometer
Eternal Threads
Touhou: Fading Illusion
Murder Diaries 1 2 and 3
Detective Kobayashi
Murder Is Game Over

Apologies if any of these are already in the list and I missed them, this list has been a godsent for me in finding interesting games to check out and would love for it to be as definitive as it could possibly be!

Some more that I forgot:
Between Horizons
Verbal Verdict
Turlock Holmes
The Order of the Snake Scale
Dyschronia: Chronos Alternate
In a Detective's Mind
Clash: Blue Mirage
The Cadet Files
Paper Perjury

@Zakdj thank you so much for all the suggestions! I also want this list to be as complete as possible so I really appreciate the help! :)

Got another batch of games. I decided to send suggestions whenever I have a substantial amount to put forward. This is A LOT, and I still doubt I've found everything I could. But more mystery games is more mystery games, and that's always a great thing.

Keyword: A Spider's Thread
Cracks Where the Light Gets In
Where's An Egg
Disco Elysium: Game Boy Edition
Crime O'Clock
Detective: Ritual of the Sea
Abscission
Back to the Dawn
Pixel Noir
Cube Escape: Paradox
Cube Escape: Paradox - Chapter 2
Inspector Schmidt - A Bavarian Tale
Red Line
Why Am I Dead: Rebirth
Aswang Detective: The Case of New York
Inworld Origins
PROZE: Enlightenment
Dollhouse
Puzzle Agent
Puzzle Agent 2
Chants of Sennaar
Overboard!
Heaven's Vault
Sethian
Norco
The Thaumaturge
Retro Mystery Club Vol.1: The Ise-Shima Case
Retro Mystery Club Vol.2: The Beppu Case
Methods: The Canada Files
Hermitage: Strange Case Files
Escape Room: Reality
Please close the doors
The Walsingham Files: Chapter 1 and 2
Yurukill: The Calumniation Games
Synesthesia
Seance
The Case of Maneki
The Firebrand
Eighteen
A Turnabout to El Dorado
The Vault
Anata o Yurusanai
Jikuu Tantei DD: Maboroshi no Lorelei
Inugamike no Ichizoku
Shin Megami Tensei: Devil Summoner
Shin Megami Tensei Devil Summoner: Raidou Kuzunoha vs. The Soulless Army
Shin Megami Tensei: Devil Summoner 2 - Raidou Kuzunoha vs King Abaddon
Sound Novel Machi: Machi
The many enteries in the Tantei Jinguuji Saburo series
Missing Parts 2: The Tantei Stories
Missing Parts 3: The Tantei Stories
J.B. Harold no Jikenbo #2: Manhattan Requiem
J.B. Harold 3: D.C. Connection
J.B. Harold: Kiss of Murder
J.B. Harold: Blue Chicago Blues
Detective Evangelion
Deka Voice
DS Nishimura Kyotaro Suspense Shin Tantei Series: Kyoto Atami Zekkai no Kotou - Satsui no Wana
Tantei Shinshi Dash!
London Seirei Tantei-Dan
Quiz Meitantei Neo & Geo
Another Time Another Leaf: Kagami no Naka no Tantei
Apathy: Narugami Gakuen Toshi Densetsu Tantei Kyoku
Tantei Jinguuji Saburo: Kadan no Isshu & Nazo no Jikenbo
Again
Tantei Gakuen Q: Meitantei Hakimida!
Tantei Gakuen Q: Kyuukyoku no Trick ni Idome!
Simple 1500 Series Vol. 59: The Suiri - IT Tantei: 18 no Jikenbo
Simple 1500 Series Vol. 74: The Horror Mystery - The Sangeki Yakata Cabin Hakushaku no Fukkatsu
Simple 2000 Series Vol. 17: The Suiri - Aratanaru 20 no Jikenbo
Simple 2000 Series Vol. 43: The Saiban - Shinmai Shihoukan Momota Tsukasa no 10 no Saiban File
Simple 2500 Series Portable Vol. 3: The Dokodemo Suiri - IT Tantei: Zen 68 no Jikenbo
Mystereet: Yasogami Kaoru no Chousen!
Camisole
Laplace's Demon
Femme Fatale
Hokkaido Rensa Satsujin: Okhotsk ni Kiyu
Fushigi Deka
Mottomo Abunai Deka
Psychic Detective Vol 1 -5
Gensou no Artemis: Actress School Mystery Adventure
Kindaichi Shounen no Jikenbou: Akuma no Satsujin Koukai
Ooe
Sanma no Meitantei
Red, Blue, and Green
BS Tantei Club: Yuki ni Kieta Kako
Hitman 3 (The Dartmoor level is based around a murder mystery)
The absurdly long list of Nancy Drew Games

@Zakdj everything added, thank you so much for finding so many games!

More obscure, similar to Hitman, MGS1 VR missions has a series of challenges called "Mystery Mode", where you solve the mystery of who the culprit behind a murder is, the final of these missions being a locked room mystery.
https://youtu.be/CcZta_mNgb0
https://youtu.be/Yg8QCbvAGGg
https://www.backloggd.com/games/metal-gear-solid-vr-missions/

@Zakdj added, thanks!

Over the past month I've been trying to get as comprihensive a list I can of games that wasn't featured on the list, here's everything I found. Hopefully next time won't be as long, apologies for how many there are!

21: Two One
26AZ: The Enigma of Shadows
404 Missing Page Detective Agency
44 The Jail
A Case of Missing Dairy
A Case of the Crabs: Rehash
A Million Murder Mysteries
A Romantic Murder
A Train Mystery
Absent in the Rain
Accuser
Ace Ventura Pet Detective: The Case of the Serial Shaver
Adventure Time: Finn and Jake Investigations
Agatha Christie 4:50 from Paddington
Agatha Christie: And Then There Were None
Agatha Christie: Dead Man's Folly
Agatha Christie: Death on the Nile
Agatha Christie: Evil Under the Sun
Agatha Christie: Hercule Poirot - The London Case
Agatha Christie: Murder on the Orient Express (2006)
Agatha Christie: Peril at End House
Agatha Christie: The ABC Murders (2009)
Akagawa Jirou Mystery: Tsuki no Hikari - Shizumeru Kane no Satsujin
Akagawa Jirou: Majo-tachi no Nemuri
Akagawa Jirou: Yasoukyoku 2
Akazu no Ma
Alice is Dead: Hearts and Diamonds
Alice Not More
Amber's Blood
Amelia Watson Case File no.420
Amerzone: The Explorer's Legacy
Amos Green's Final Repose
Another Lost Phone: Laura's Story
Another Time Another Leaf: Kagami no Naka no Tantei
Arcadia Files: Clyde
Arkham Detective
Asou Youichi no Jikenbo: Dochiraka ga Kanojo wo Koroshita
Big Ear Detective
Black Circle
Blood On The Thames
Blue Heat: The Case of the Cover Girl Murders
Blue Madonna
Borderline Detective
Bosch's Damnation
Call of the Golden Valley
CAMEO: CCTV Detective
Card Detective
Case #1472
Case 32
Case Files: The Death of Paulette Williams
Case of the Mysterious Death of Keiko Haraeda
Casebook 1899 - The Leipzig Murders
Cashand Case
Cat Detective
Cat the Ripper: 13-ninme no Tanteishi
Chains of Judgment
Cheree: Remembering My Murder
Chicken Police: Into the Hive!
Chizome no Hana
Chocolate Carol
Chook & Sosig: A Case of Murder
Chotto xx na Watashi no Nichijou: Kiki Dasshutsu!? Gyakuten no Nazotoki Life
Chronicles of Mystery: The Scorpio Ritual
City of Lost Hope
Cold Case Summer
Condemned 2: Bloodshot
Condemned: Criminal Origins
Cosmic Connection
Counter Clock Case
Cradlemoor
Crewmember Pigeon and the Case of the Burgled Buttons
Crime and Punishment
Crime Investigation
Crime or Punishment
Crowhille: Detective Case Files VR
Crowns and Pawns: Kingdom of Deceit
CSI games
Curious Cases
Cyberpunk Detective
DAEMON MASQUERADE
Dare ga Humpty wo Koroshita no?: Lizzie, Futatabi Tantei ni Naru
Dark Fall
Dark Tales: Edgar Allan Poe's Murders in the Rue Morgue
DarlingHoney!
Dasha Vasilyeva: The Personal Case of Catwoman
Dead Drop
Dead Meat
Deadly Attachment
Death by Begonia
Death Game Hotel
Death Is A Guest
Death of the Artificer
Delaware St. John: Volume 1 - The Curse of Midnight Manor
Delaware St. John: Volume 2 - The Town with No Name
Delaware St. John: Volume 3 - The Seacliff Tragedy
DETECTIVE - The Motel
Detective AI
Detective Bass 2: The Case of the Stolen Pearls
Detective Bass: Fish Out Of Water
Detective Bot
Detective Butler and the King of Hearts
Detective Case and Clown Bot in: The Express Killer
Detective Clean
Detective Conan
Detective Conan: 3-nin no Meitantei
Detective Conan: Aoki Houseki no Rinbukyoku - Rondo
Detective Conan: Daieiteikoku no Isan
Detective Conan: Kanzen Suiri! Kazu to Zukei no Nazo
Detective Conan: Kieta Hakase to Machigai Sagashi no Tou
Detective Conan: Kiganshima Hihou Densetsu
Detective Conan: Marionette Symphony
Detective Conan: Norowareta Kouro
Detective Conan: Phantom Rhapsody
Detective Conan: Saikou no Aibou
Detective Dave
Detective Dotson
Detective Fantasia DX
Detective Fantasia: Excalimurder
Detective From the Crypt
Detective Gallo
Detective Gman
Detective Hayseed
Detective Patch
Detective Ridelle
Detective Rosie Morgan: Death at a Dinner Party
Detective Rosie Morgan: Murder on the River Thames
Detective Story: Reporter
Detective Time
Detective Tycoon
Detective Zhuge
Detective: Minerva Case
Detectiveland
Devastated Path
Digimon Story: Cyber Sleuth
Digital Exorcist
Digital Exorcist Case_(0);
Diorama Detective
Doki Doki AI Interrogation
Doll Recollect
Duppy Detective Tashia
Dynasty Detective
Dziedzic: A book of unanswered questions
East Side Story
Echo Night
Echo Night 2: Nemuri no Shihaisha
Echo Night: Beyond
Echo Night: The First Voyage
Eikoku Tantei Mysteria
Extraordinary Detective Marshall
Face 2 Face
Facility 47
Fantastical Mystery ADV : Ultimate Jumbo Jet Murder Case
Fantastyc Murder Mystery
Feline Forensics and the Meowseum Mystery
Fingerbones
Five Day Detective
Flower, Sun, and Rain: Murder and Mystery in Paradise
Folklore
Follow the meaning
Fukakutei Sekai no Tantei Shinshi
Fukakutei Sekai no Tantei Shinshi Origin!
GENBA no Kizuna
Geospots
Getsumen no Anubis
Gizoku Tantei Nosuri
Graces: Posthumous wish
Graywood: Noir Detective
Grim Fandango
Grim Fandango Remastered
Gyakuten Vocaloid
Phoenix Wright Ace Attorney - Trials After Justice
Hankou Shashin ~Shibarareta Shoujo-tachi no Mita Mono wa?~
Hateful Days
Hector: Badge of Carnage - Full Series
High Stakes
Home (By Benjamin Rivers)
Home: Postmortem Edition
Hope Springs Eternal
Hoshikage no Yakata Satsujin Jiken
Hotel Perkkow and the Two Vegetarian Werewolves
Hyperrail Detective
I am Your Lawyer
Ice Cold Case
Ikatan: Ikamono Tantei
Inspector Detective: Private Eye
Inspector Waffles
Inspector Waffles Early Days
Internship Detective
Intersection
Investigator and the Case of the Unconventional Weapon
Jaaman Tanteidan Marine-Gumi: Hi Jigoma Sousa Fairu
Judge Dee: The City God Case
Just Two
Kagiana Satsujin Jiken
Kamaitachi no Yoru Advance
Kamaitachi no Yoru Triple: Mikazukishima Jiken no Shinsou
Karpatia: Order Of The Comet
Kill The Shadow
Kona
KONA Project
Kotodama: The 7 Mysteries of Fujisawa
Last Case: The Disappearance of Amanda Kane
Later Alligator
Law and Order games
Laws of Nadragia
Little Locked Rooms
Little Locked Rooms
Little Problems
Locator
LumineNight
M.S. Salmon
Machi: Unmei no Kousaten
Majin Tantei Nougami Neuro: Battle da yo! Hannin Shuugou!
Majin Tantei Nougami Neuro: Neuro to Yako no Bishoku Sanmai
Manga de Tantei Mystery
Maria-sama ga Gyakuten
Matantei Loki Ragnarok: Gensou no Labyrinth
Meitantei Conan & Kindaichi Shounen no Jikenbou
Meitantei Holmes: M kara no Chousenjou
Meitantei Konan: Tantei-ryoku Torēnā
Meitantei Shikkaku na Kanojo
Memory Rewind
Methods: The Illusion Murders
Mississippi Satsujin Jiken: Murder on the Mississippi
Mizen Tantei: The Protea Cases
Montgomery Fox and the Case of the Missing Ballerinas
Moonflower
Mr. Hack Jack: Robot Detective
Murder Mystery 2: Criminal Case
Murder Mystery 3: A Life of Crime
Murder Mystery Case 3: Who Killed Brett Penance - The Environmental Surfer
Murder Mystery Case 4: Who Killed Taylor French - The Case of the Undressed Reporter
Murder Mystery- Detective Investigation Story
Murder On Space Station 52
MY FATHER LIED
Mysterious Mystery, EP 1: The Duo Dilemma
Mystery Case Files: 13th Skull
Mystery Case Files: Madame Fate
Mystery Case Files: MillionHeir
Mystery Case Files: Ravenhearst
Mystery of Rivenhallows
Mystery of the Murderous Dreams
Narcotics Police: Crime And Punish
NCIS
Never 7: The End of Infinity
Nick Bounty: A Case of the Crabs
Night Detective: Decrepit Manor
No Recollection
Nobody Wants to Die
Noir Detective
Notebook Detective
Omoikkiri Tanteidan Haado Gumi: Matenrou no Chousenjou
One Last Dinner
Orly Kuukou Satsujin Jiken
Orten Was the Case
Oshiri Tantei: Pupu Mirai no Meitantei Toujou!
Ouma ga Toki
Oumagatoki 2.
Paper Pilgrim: The Crystal Case
Perfect Detective Manual
Perry Mason: The Case of the Mandarin Murder
Phantom Detective
Pirate Fox Detective: The Case of The Conspicuous Klawz Crew
Polgar: Magic Detective
Police Girls on the Case!
Port of Call
Post Mortem
Pro Yakyuu? Satsujin Jiken!
Profound Red
Provisional Detective
Psychic Detective
Quarantine Diary
Rainswept
Real Crimes: The Unicorn Killer
Reijou Tantei: Office Love Jikenbo
Remedy
Rocky Rhodes and the Cracked Case
Sam & Max Hit the Road
Sam & Max: Beyond Time and Space (Original and Remaster)
Sam & Max: Save the World (Original and Remaster)
Sam & Max: The Devil's Playhouse
Sam & Max: This Time It's Virtual
Sam Mallard: The Case of the Missing Swan
Santa Fe Mysteries: Sacred Ground
Santa Fe Mysteries: The Elk Moon Murder
Scorch
Scratches: Director's Cut
Searchbar Detective
Seven Sacrifices
Shades of Black
Sherlock Holmes Consulting Detective: The Case of Banker's Final Debt
Sherlock Holmes: The Case of the Beheaded Smuggler
Shichisei Tantei Club: Koganemushi-tachi no Kisou
Shin Kamai-tachi no Yoru: 11nin-me no Suspect
Shinoda Shinjuku Tantei Jimusho Karajishi Botan
Silver Creek Falls: Chapter 1
Silver Creek Falls: Chapter 2
Silver Creek Falls: Chapter 3
Sixth Grade Detective
Small Town Detective
Snail Detective
Solve The Case
Sound Novel Evolution 2: Kamaitachi no Yoru Tokubetsu-hen
Space Detective: The Case of the Rebel Robot
Staffer Reborn
StafferCase: A Psychotic Mystery Adventure
Star Apprentice: Dazzling Danmaku Detective
Still Life 2
Strange Case: The Alchemist
Syberia 3
Syberia II
Syberia: The World Before
Tantei Kibukawa Ryousuke Jiken-tan vol 1-13
Tea For Two: A Detective Logan Game
TEEFAX: Cold Case
The Agency: Chapter 1
The Agency: Chapter 2
The Beresford family
The Birdwatcher
The Case of Andrew D.
The Case of the Cautious Condor
The Case of the Muffin Diver
The Colour of Murder
The Dead Case
The Deed
The Deed II
The Deed: Dynasty
The Detective
The Detective (1986)
The detective ChuLin
The Detective Reaper Invites
The Diamond Mystery in Rosemond Valley
The Diary (2024)
The Elliot Brown Case
The ever-changing case of the unpaid rent
The Game Maker
The Ghosts of Hackney Mills
The Good Life
The Item Sagashi: Joshikousei Tantei Shinjitsu no Jikenbo
The Last Case of Benedict Fox
The Magnilo Case
The Missing: J.J. Macfield and the Island of Memories
The Mystery of the Hudson Case
The Operator
The ordinary case of Margaret Luoni
The Precinct
The Real Faces of Vtuber
The Roottrees are Dead (2024)
The Samaritan Paradox
The Shell Part I: Inferno
The Shell Part II: Purgatorio
The Suicide of Rachel Foster
The Vampire(?) Detective and the Case of the Lying Maid
The Vigil Files: Case 1
The Wolf Is Dead
There is NO PLAN B
Time Stand Still
Times & Galaxy
Timeshift Detective
Todo Ryuunosuke Tantei Nikki: Kohaku-iro no Yuigon
Tokyo Detectives
Tokyo Psychodemic
Touch Detective 3
Turnabout of the Golden Witch
Uncover the Smoking Gun
Underdog Detective
Unreachable
Urban Myth Dissolution Center
Virtual Murder 1: Who Killed Sam Rupert?
Virtual Murder 2: The Magic Death
Welcome to Lightford
What Awaits, Aleksey?
What happened to Kate
What have you done, Father?
Wildwood Down
Wolf Peak: The Case of Ruth Choi
Yamamura Misa Suspense: Kyouto Ryuu no Tera Satsujin Jiken
Young Detective
Your Friendly Neighborhood Vampire Detective
Zukkoke Threesome: Drama Murder Case

@Zakdj All 300+ games added! Thank you as always for finding such an extensive list of games!