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!