Not so well-known games, but really good

Binary Domain is one of them, awesome gameplay and great story.

try Unepic!

Atlantis: The Lost Empire - Seems like a run-on-the-mill 3D action adventure platform... whatever, but it's just so great. Has all the clichés from the book for a generic game, but it's done so well, it's still among my favourites. Don't expect it to follow the film too closely though, but surprisingly, it's just great. Wish there was a PC port.

Bad Mojo - Hard to sum up, but here goes. You're a man turned into a cockroach due to a cursed medal, and you have to embark on gaming's biggest fetch quest to regain your true form. Its FMV cutscenes are delightfully over-acted, and the game is just so gross. I mean, it's an apartment up real close, what would you expect? Otherwise, you'll never play anything like this anywhere.

Giants: Citizen Kabuto - TPS/RTS hybrid that works. And it has jetpacks, and sometimes its jokes are actually funny.

Viriax - One of the best free indie titles out there. It's hard as nails, and there's nothing quite like it out there. Completely original, I love it.

Flywrench - One of the best free indie titles out there. It's hard as nails, and the... waitaminute. Yeah, it's another indie darling out there, also free. This one's among my all time favourites too.

Okay I got bored, take these and enjoy.

Have played Alien rage for a bit. MP is Kal drogo dead, but its quite good. Frustrating as hell, but i think its decent.

Deception 3: Dark Delusion

Super Panda Adventures, really good metroidvania. Panda needs more love.

I recently made giveaways for these and would recommend them:

Sproggiwood
Caves of Qud
Dungeon Souls

Darkest Hour
Very good 1ww-early cold war grand strategy.It's a bit old but still very good

UnderRail : a really great post-apocalyptic isometric RPG.
Also you can choose between two systems of experience gain : a classic system and one that rewards exploration rather than combat

My list:
Agarest: Generations of War - HUGE tactic jrpg, involves dating and then playing as your offspring.
Ballpoint Universe: Infinite - solid horizontal shooter with really nice aesthetics.
Consortium - RPG/Adventure/FPS. You have to talk to your crewmates and try to prevent an international crysis.
Cloudbuilt - nice looking run n gun. More run less gun.
Double Dragon Neon - DUH.
Strider - Double DUH.
Whole Endless series - Awesome 2 4x games and one interesting roguelike/tower defence. Known but not well enough, since Legend hasn't topped Civilization Beyond yet.
Inquisitor - oldschool rpg from Czech company. You can torture people and spend over 100 hours following the story and fighting enemies.
Karmaflow: Rock Opera Videogame - title says it all.
Merchants of Kaidan - Merchant sim.
Mitsurugi Kamui Hikae - hawt babe slashes demons with katana, you can't go wrong with this one.

Fight The Dragon-

Awesome Mix of Player Created Database of over 1000+ hours and Randomly generated dungeons and levels to grab the best loot, check it out! its well fun.

Timeshift
Judge Dredd: Dredd vs Death
Bet on Soldier

Nihilumbra - I absolutely adored the story portion of the game, and for those who enjoy a real challenge, what comes AFTER the story is incredibly challenging!
Zafehouse Diaries - Oh my gosh, so good! _ Absolutely addictive turn-based strategy/survival game.
A Vampyre Story - The humor is a bit on the juvenile side, but I enjoyed the heck out of this point-and-click.
Sacra Terra: Angelic Night - I was surprised at how good this IHOG ended up being
(All of the above links to go my reviews -- scroll up one post to see where you can get the games)

(All of the below have reviews, too, but I'm too lazy to link them -- you can find the review links HERE.)
Nevertales: The Beauty Within - Voted the best IHOG of 2013, and for good reason!
Shiver 1: Vanishing Hitchhiker - Deeply environmental IHOG, truly shiver-worthy
Ghost in the Sheet - I don't know what it was about this game, but I enjoyed it SO MUCH! I don't know if it's available anymore.
Runespell Overture - Battle solitaire/RPG! Who'd a thunk it would work so well?
ENSLAVED: Odyssey to the West - This game really deserves more attention... I would've immediately started it over again if I hadn't had so many games in my backlog!
Max: The Curse of Brotherhood - I adored the gameplay in this platformer, and the graphics are outstanding!
Tormentum: Dark Sorrow - a casual adventure game that is both dark and fascinating to look at. Two possible endings!

I've reviewed WAY more IHOG's than anything else, but if you scroll down to the second post of my reviews, you'll find the most-recent games I've played, which are more mainstream for the Steam crowd.

I'll show you a few steam games that have been released within the past year that i've been given the chance to review and have really enjoyed!
Contradiction Store Page My Review
Skyforce anniversary Store Page My Review
Color Guardians Store Page My Review

"Hostile Waters" only one I can think of right now...a true gem

Letter Quest
That game really surprised me. Didn't expect to enjoy it that much.

As usual, nobody mentions poor Legend Entertainment and their whole pile of top games;-(

Some games with pretty good story are
Ether One - You play as a Restorer and try to alter the memories of a patient with dementia in order to help him.
Fahrenheit: Indigo Prophecy - You must uncover the man behind the mysterious murders done by strangers who don't remember anything about them.
Remember Me - You play as Nilin who must escape prison and regain her memory after it was erased by the Memorize corporation. There's a lot more to it and I might've explained it poorly.

To The Moon: http://store.steampowered.com/app/206440/

Bastion.

Septerra Core, still hands down one of my favorite RPGs. It's an older game but the story is decent and the combat is easy to get into, the graphics are a bit dated though.

http://store.steampowered.com/app/253940/

Warhammer 40 000: Chaos Gate comes to mind since it came to GOG couple of days ago :) This rough and surprisingly less known gem just has it all (allthough it is a bit dated on visual side):
-Fighting against Chaos forces as underdog, especially if you lose precious battle brothers in earlier missions, is so rewarding!
-Manage your Space Marines: select different load outs, merge squads, change their names to suit your needs
-Epic music which would be good enough for the Emperor! Really!

Chaos Gate: http://www.gog.com/game/warhammer_40000_chaos_gate

You can also check Final Liberation, this games big brother since it offers you a war on bigger scale: http://www.gog.com/game/final_liberation_warhammer_epic_40000

Severance: blade of darkness, Revenant, Cultures and Warlords Battlecry 3 from the old games that I wish they had sequels... Also Knights of Honor.

Cry Of Fear, a psychological horror game which started out as a mod for Half-Life 1, and became a standalone game. Even though the game is not too long and it's a little linear, it has a high replayability due to the multiple endings, the mindblowing story, the great soundtrack, which always fits the atmosphere and, of course, the unlockables. In my opinion it's great graphically, given that originally it was a Half-Life 1 mod and used it's engine.

And what's the best of all? It's FREE!

Rise of Nations.. literally nobody I know is really still playing it. It's like it just faded back into old game graveyard of obscurity.