Recommend hidden Gems

Reus-a timed god game, its a bit limited in scope per playthrough but has quite a bit of replay value

Chantelise-fun light-hearted action RPG

Psychonauts-an old game that has held up well over time, if you've never played this you owe it to yourself

the void

Aquanox and its successor. Someone compared it to Freelancer, and it's very similar, minus the trading.

TRON 2.0, a real gem.
But i'm not sure that this game is available in Steam. Or somewhere else...

recettear an items shop tale...

La-Mulana, I guess (If it can be considered a hidden gem). You could go for GunGirl 2 (One of my favorite freeware games out there. You could go for Shogo (If you're into the FPS genre). The first two Fallout games are great as well. If you're into RPGs and Flash Games, you could try Mardek RPG and Epic Battle Fantasy, and if you like Tower Defense games, you could go for Gemcraft Labyrinth. Chantelise (Which is kinda like Ocarina of Time in terms of gameplay). The Y's Franchise is great as well. Those are all the hidden gems I can think of right now.

FTL

Papers, Please

Edna and Harvey: Harvey's New Eyes

:D

Secret of the magic crystals

Tobe's Vertical Adventure.
Super Brother's Sword and Sworcery EP, if that's considered one. I know the first one definitely is.

Trackmania

Bump

If you like indie games, I highly recommend:
Brothers - A Tale of Two Sons - it's on sale now, but you need an XBOX 360 controller to play it
To the Moon
The Bridge
Botanicula
The Tiny Bang Story
The Book of Unwritten Tales

King of Dragon Pass

Play Darkout! It's like Terraria or Starbound, but it's more darker, and story driven. Although it has randomly generated maps, it IS story driven. Or play Paranautical Activity. If you played ( and loved ) Binding of Isaac, you should play PA. Or if you like horror games, you should try Paranormal.

Well there are a few here.

I heard Marlow Briggs and the Mask of Death was good, I picked it up but haven't played it yet

Psychonauts is the most underrated game ever. It's funny, it's fun, it's weird and it can be really dark. And it's really cheap. So, do yourself a favour and buy it.

Super House of Dead Ninjas and Rune Classic.

And Yet It Moves

Great art style, lovely ambience and the world shifting mechanics work really well

Rondo of Swords is a really interesting DS game. It's a twist on the tactical RPG genre where you run through enemies to attack rather than stand next to and hit them. Also has a really good moral choice through gameplay, rather than just asking you if you want to be good or bad. I never see anyone talk about or even mention this game and that makes me sad.

Unepic. Very fun RPG game with about 50 hrs of campaign, and then endless gameplay after.

Maybe not that unknown but very underrated (in my opinion): Alpha Protocol and Binary Domain.

Under the Ocean? Not too sure what I think of this one.

King's bounty series. Addictive as fuck.