Gunpoint. Story based detective game where you solve a murder. Gameplay mechanics make you feel like a badass. You can pretty much finish it in a single sitting but its great.

Heat signature. A stealth based top down bounty hunter game with roguelike elements. Really well done. Made by the same guy that made Gunpoint.

Neo scavenger. A murder hobo roguelike with a surprisingly long storyline.

Super house of dead ninjas. Great fast paced platformer where you’re a badass ninja. Great to pick up and play in short bursts.

Fez. 2D exploration platformer with to change the perspective. Pretty chill and has a cool art style

More well known games that I’ll list anyway in case someones looking for some awesome ones:

Super meat boy

Project zomboid

FTL

Celeste

Crypt of the necrodancer

Enter the gungeon

Spelunky

Noita. Saw it mentionned in this thread and I am seconding this. Great game. But brutal as fuck.

Cave story. A classic. And it’s free.

Owlboy. Took the developer like 10-15 years to make. I’ve heard good things but I’m only just starting to play it.

Also pro tip: if you want more recommendations go look at what speedrunners are playing. People that spend that much time playing a single game over and over generally choose very good games to play.

Parkitect - an amazing RCT spiritual successor with cute graphics, some new mechanics (covering operational buildings and logistic routes). I have 100+ hours in it with my wife. It's such a chill experience.

Nine Parchments - its a dual stick isometric shooter with wizards and elemental spells from the creators of Trine. Great co-op, unlockable characters/spells and creative mechanics. You can combine elements and the spells affect everyone, so for example a poorly placed healing spell can restore enemies health, or a misplaced fireball can hurt fellow players. Great fun!

Wildermyth - turn-based rpg with multiple characters and bite-sized modular quests and random encounters. The storytelling is simply amazing and each campaign plays out over a certain amount of time. The heroes age, retire, their kids can become adventurers as well. They can fall in love, compete, or based on the player's choices even become other creatures or die heroic deaths which will also change how the story plays out. The art style is really nice and unique. I had many hours of fun with this one.

Distance - an arcade racer that plays like a good 3D sonic game, has a cryptic story, and has elements of horror. Completely bonkers combination but it works super well.

Thumper - another very fast paced game, but also a rhythm game. The devs label it as "rhythm violence" and it fits. The music is percussive and ambient, mostly consisting of the sounds of you slamming through turns and hitting the a button with ferocious intensity. Levels can take well over 30 minutes.

The Beginner's Guide - might be more well known but imo this is a must play for anyone who does anything creative. It's a two hour walking sim, but I feel like it's a story best told as a game.

Antichamber is hidden gem or simply forgotten? I don't know how much attention it got in its time.
It's a puzzle platformer but I was feeling my brain bend the whole game. And at the same time I never felt like the new mechanic was explained too little or something was artificially dragged out. Very good design.

IMO it was better than Portals

Starsector: It's an Elite style open world space game. What makes it special is that it's been in constant development for over a decade and has a crazy number of ships, weapons, lore and features. And a vibrant modding scene.

Also the devs are vehemently against DRM, so the only place you can buy the game is their own website. Or not buy. They put the full version up for anyone to download.

In decreasing popularity (estimated by me):

• Creeper World: A mix of tower defense and rts (with pause function) against a ever expanding goo called creep. The fourth installment is 3D and the next one will be a side-view spinoff.

• Tales of Maj'Eyal: Quite popular among the people who are into traditional roguelikes, but I very very rarely see it mentioned outside that community. It's definitely the (nearly) traditional roguelike I put the most time into thanks to its class/ability system that bridges the gap between roguelike and turn based rpg really well.

• The Captain: Technically not indie as it was published by Tomorrow Corp (of World of Goo/Little Inferno/etc. fame) instead of the devs themselves. A mix between old school point and click game, but as a highly episodic space adventure. You travel from planet to planet on an overarching mission and each planet has its own interactive short story. Some are longer, some are very short and you never quite know what you'll find before you land. All of the short stories have multiple endings depending on how you tackle the moral dilemmas it throws at you.

• Infinity Wars actually released before the rise of Hearthstone and also before the popular Avengers movie of the same name. It is to this day one of my favorite digital TCGs, and I played so many of them. Before I get into the main thing that I love about it, I wanna mention that every single card's base version (colorless) is free, anyone can build any deck for free the moment they pick up the game and be 100% competitive with everyone else. The only thing they monetize is bling. Unlike in most mainstream TCGs both players do their turns at the same time in secret, once they both lock in, their moves play out. This gives way for some insane mindgames and outplays that eclipse those in any other TCG I've played. It is a bit rough around the edges, so it might be more of a "hidden diamond in the rough" than a hidden gem.

• Bombernauts is a really fun party game. To sum it up in one sentence: "Imagine if Bomberman was a platform fighter." If you have friends to play with it, buy it on a sale, crank powerup drops up to the max (they stack, which took us hours to figure out), maybe download a mappack and I'm sure you'll have a blast if the trailer looked any fun to you. There's virtually no chance to play it with strangers through as it is super dead.

• Lastly I wanna give a shoutout to Clonk. Clonk is (or was) a 2D sidescrolling game-series that is visually reminiscent of Lemmings. The gameplay is a sort of mix between Minecraft or Terraria (predating it by many many years) and very very very low-pop RTS. It's a mission based game where you control around 1-3 Clonks (the lemmings) and has full online multiplayer support. The missions can range from "build a base in this active volcano", "take out the enemy team's castle", "win this wizarding duel" to "build a bridge across this canyon". What made it truly unique was the community and community creations though. It was created with the explicit purpose to be customizable and users made many, many different maps and modes. It was to me what Minecraft was to the kids in the generation after me (without all the content creators, of course). Some people made an entire RPG in it. Others made what was essentially Among Us, just to give you an idea. Sadly the spiritual open source successor Open Clonk could never recapture the magic for me, and I guess I'm not alone in that because it pretty much died around 5 years ago. If I could make one game popular overnight, it would be Clonk. It did warm my heart to see that some of the celebrated custom map/mode creators from back then ended up getting into gamedev. One of the games developed by someone I remember from back then is Vintage Story.

Holy fuck I rambled a lot about Clonk and I still feel like I'd have so much more to say but this isn't the most fitting thread for that.

Crosscode is one of my favourite games of all time. It's an immensely charming action RPG heavily inspired by the 2D Zelda games. It has some absolutely insane combat and surprisingly challenging puzzles. The story is also very good and really touching at times. The devs spent 7 years making this game and I feel like it never got anywhere near the attention it deserved.

It's just $20 on steam AND it has a free demo, so there's no reason not to check it out!

Ouroboros - an RPGmaker game where the protagonist is trapped in a looping simulation and tries to escape without alerting his captors. Short and sweet, perfectly executes the power fantasy of being a hyper competent rational character who's gone completely emotionally numb after living for thousands of years. It's an adult game and features some sex scenes but they're not important and I think they can even be turned off. It goes on an 80% discount every steam sale.

Receiver is pretty good. You have to clear the slide, and remember to count bullets, did your own jams, and otherwise it makes shooting more of a simulation rather than an arcade.

Aquaria is a very expansive Metroidvania with great visuals, creative encounters, and excellent music. Certainly one of my favorites growing up.

• To The Moon: Absolutely heart breaking.
• Tales of Maj'Eyal: An incredible rogue-like with 30+ classes and God knows how many achievements.
• Cataclysm Dark Days Ahead: Apocalyptic rogue-like. Zombies, bandits, aliens and Lovecraft shit. Want to raid a dojo? Learn Judo from a book and proceed to race around town on a pair of rollerblades practicing on the undead? Feel free.

Levelhead is a fantastic mario-maker esque platformer. The official campaign is a little over 10 hours long and is pretty good but its main draw is its incredible level editor and infinite number of quality levels online. I can't recommend it enough. Sadly it never got as popular as it should have but there's still a massive backlog of online levels to play.

Someone else mentioned Distance and I agree. It's a futuristic racing game with some horror elements. The campaign is short, but there's a great amount of levels in the workshop. The multiplayer modes are also pretty fun if you can grab a few friends (there's split-screen too).

Inkbound is launching from early access soon and while I wouldn't say it's the greatest roguelike out there, it's a lot of fun and very unique. It's essentially a co-op turn based RPG where you and other players play all your turns at the same time. I've played a lot of singleplayer too and the game feels well balanced there.

Voxelgram is Picross 3D for PC. Must-have for people who like nonograms.

Shadows of doubt is a sandbox detective game. You are a detective and you have to solve crimes, which are totally randomized. What makes this interesting is that the world does not stop:

• the NPCs actually have daily routines
• the murderer might not stop killing
• you can talk with anyone
• and so much more

It is truly a sandbox! I havent played it too much yet, but i feel if i really start playing it, then i will skip going to bed!

Griftlands doesn't get as much attention as I think it deserves. It's everything Slay the Spire offers, but better. With plot and characters and two decks to balance.

Unciv for Android. It's basically Civilization 5, but FOSS.

Shoutout to Iji, too. Amazing soundtrack and lots of replayability. It's an old game by now, but it's also free. Sidescrolling platformer, killing is optional.

Assault Android Cactus. Dunno how well known the game is, but it's one of the best twin stick shooters/bullet hell I've played, with the android girls full of charm.

Mindustry

Hacknet. You play as a novice hacker who investigates the disappearance of a character by hacking into other people's computers to gather information.

The hacking mechanic is fairly realistic and requires you to use the terminal a lot, so it really makes you feel like a hacker. Pretty short and sweet game, and the soundtrack is pretty good as well

Pick your favorite genre:
What The Golf? - A wild and hilarious mini golf game
Miasmata - A horror/cartography game... you heard me right! You have to use the intuitive in-game triangulation system to create your map and find your way around an island while being stalked by a creature as you search for a cure to your mysterious ailment
Rain World - 2D Metroidvania where you're a little slugcat in a post-apocalyptic world filled with dangerous predators and lethal rainstorms
Diaries of a Spaceport Janitor - Life sim where you're a janitor in a bustling Star Wars-esque spaceport living on the edge of poverty and dreaming of more
One Shot - Emotional story-driven game in a similar vein of Undertale
Night in the Woods - Not that hidden, but I absolutely love this one. Narrative life sim about someone returning from college to their Appalachian hometown and mysterious things are going on
Dreamfall Chapters - Adventure game that spans a sci-fi dystopia and fantasy world with many interconnections
Grow Home - 3D platformer where you're a little robot growing giant beanstalks to return to your spaceship
There Came An Echo - Tactical strategy shooter you control only with your voice

It’s old enough that I can’t attest to how hidden it was/is, but Superbrothers: Sword and Sworcery is likely the greatest 3 hours I’ve spent in a single videogame. It’s chock-full of confidence and style and atmosphere. The story is nothing unique but the presentation is everything. Pixellated graphics contrasted with vivid sound design and a glorious soundtrack. I love everything about it.

Citizen Sleeper - From the same publisher as The Pale Beyond, it's another one of those story games that borders on visual novels. It's a game about precarity and personhood set on an anarchic, decaying space station. Gorgeous art, fantastic soundtrack and it's uniquely hopeful. Might be favourite game of the last few years.

Cloudpunk - A cyberpunk driving/walking simulator with a good story, great voice acting, LEGO-inspired graphics, and a Blade Runner inspired soundtrack. It’s dripping with atmosphere and I wish I could play it again for the first time.

Plate up : a rogue like kitchen survival game can also be multiplayer , survive as many days as you can getting more customers but also more kitchen gadgets

Back back hero: rogue like dungeon delve with pack management and new story mode where you rebuild a town .

Both are surprisingly addictive and consume my dreams

A Robot Named Fight - "Metroidvania roguelike focused on exploration and item collection. Explore a different, procedurally-generated labyrinth each time you play and discover randomized power-ups to traverse obstacles, find secrets and explode meat beasts." Links: Steam - Website (It is also available on Switch, link on website)

I have almost 500 hours of playtime and still go back to it every now and then. Really awesome game with superb music, graphics and feel.

What's extra cool is that the lone developer open-sourced the game code, available here: OpenARNF on GitHub Sadly I've yet to see any mods, spinoffs or anything else come from it.

Signalis

Antichamber

Cave Story

The Beginner’s Guide

Uplink

Hypnospace Outlaw

Exit Fate

The Red Strings Club

Oolite

LocoRoco (not an indie gem but forgotten)

Hypnospace Outlaw

Iconoclasts - really nicely made metroidvania with pixel graphics

Tametsi - a collection of handmade Minesweeper puzzles with additional twists and mechanics. Extremely cheap on Steam

Gunfire Reborn - roguelite FPS with Borderland-ish graphics, decently made 4 man co-op (unlike Risk of Rain 2, you can actually revive teammates that got knocked down immediately) and a lot of difficulty scaling. Notably, still gets new content, both free and paid DLCs (those add new classes and some new weapons)

Edited to add another: Opus Magnum - an automation/optimization puzzle game with alchemy theme. Supports user-created puzzles through Steam Workshop

• Beacon Pines -- a charming mystery story with anthropomorphic animals. Has an interesting take on the visual novel formula by having you unlock new dialogue choices as you progress through the story; that way, you naturally explore different paths the story might take. Night in the Woods and (possibly) OneShot fans might like this one.
• Oolite -- a solid FOSS remake of 1984's Elite. Has a bunch of mods for it; some expand the gameplay quite substantially.
• Orbiter Space Flight Simulator -- imagine a Microsoft Flight Simulator game, but you're going to space instead. Or Kerbal Space Program, but without the rocket building mechanic. That being said, KSP fans (and fans of space in general) should enjoy it.
• Transcendence -- Star Control II meets Rogue. A cult classic in the space sim genre that's been in development since 1995. Space dogfighting, trading, mining, smuggling etc, but also traditional roguelike stuff like unlabeled barrels and containers (= undiscovered potions) and permadeath (optional). Highly moddable, uses XML as the modding language. Has a free version (see link) and a Steam release, which includes the paid expansions.

Phoenotopia: Awakening – an amazing metroidvania-related game. Relatively more popular than the other games I list, but is honestly one of my favorite games of all time.

Vision: Soft Reset – a metroidvania, but you can travel backwards and forwards in time and this really matters for gameplay.

Bombe – Minesweeper, but instead of solving the puzzles manually, you create rules ("if there is a cell with the number N and there are N empty cells around it, mark them all as mines") which the game applies automatically.

SOLAS 128 – a puzzle game where you redirect signals in a huge machine, just a great experience if you like puzzle games.

I'll add Noita to the list of hidden gems. And Baba Is You.

I had a great time with a couple card battlers last year, Cobalt Core and Nitro Kid.

Cobalt Core has a similar presentation to FTL, with a turn-based format instead. Plenty to do in it, great soundtrack, charming writing.

Nitro Kid is on a more traditional 2D grid with an isometric viewpoint. It appealed greatly to my love of 80's settings, but I'd wait for a sale as it's thin on content.

Hmmm... how about the Rusty Lake games? They're weird. Or maybe Milk Inside a Bag of Milk Inside a Bag of Milk? Adventure puzzler and VN respectively.

I probably have a few more if I think about it. My friend and I randomize my steam list to decide things to play and there were quite a few interesting ones I got from who knows where-- bundles and bundles.

I've never heard or seen anybody else mention Suzerain. It's like a choose-your-own-adventure political strategy game, which is pretty unique. You are the new leader of a fictional nation wrestling with corruption. Your decisions will affect the outcome. Game is only $6 on Steam right now and is well worth it.

Also worth mentioning Ostriv, a beautiful city-builder in which you build an 18th Century Ukrainian village, complete with individual little villagers wearing their villager clothes. It's lovely and made by ONE GUY, as best I can tell? Also, last I saw, the entire game was somehow under 1 GB, if I remember correctly. It's absurd.