What are some good puzzle/thriller games that have a good atmosphere?

Have you ever played anything in the Professor Layton series for Nintendo? Great games.

Anti-Chamber is one for Portal fans for sure, recently released and very mind-bending. (PC/Steam) For Amensia fans, the companies previous "Penumbra" series is a obviously choice (PC). As well as Nintendo's much praised, but mostly overlooked Eternal Darkness game. (Gamecube) I also have a voice behind me saying the "999" on the DS has a superb horror atmosphere.

There's a game called Lacuna that BITS, Pilani students have built and designed from scratch. What makes it different from other puzzle solving games is that it comes with a game interface that's not only fun to play but is also mentally stimulating. Even if you aren't in the mood for a competitive game it'll be fun to play. https://www.facebook.com/lacuna.bits http://www.bits-apogee.org/lacuna/

There is an iOS game named The Room that has great atmosphere. I'd recommend you play it with iPad and headphones.

http://www.wikiwand.com/en/Oxenfree - Release Date(January 15, 2016) - Developed By(Night School Studio) - Art of Play(Side scrolling, Click and choose, Decision making) - Theme - Supernatural End Biting Thriller. I happened to finish this game in 4:30 hrs, short enough but a long lasting satisfaction. Well, if you are quite familiar with a game called Alan Wake, Oxenfree does lack the 3d GFX and beautiful environment but it surely does have an enthralling  end. Pros : Good script play and immersive story line. In a few minutes, you start imitating yourself as a protagonist in the game. You feel as the one who is speaking and not the AI where the dialogues perfectly blend with your cognitive process. Admirable soundtrack. Subtle thrills and mind bending scenes.

Not really a thriller but it was a fun puzzle game that had a Portal vibe to it: http://store.steampowered.com/app/203730/