I really have a thing for that atmosphere of desolation and loneliness found in the Metroid Prime games and Shadow of the Colossus. Being alone in a strange world, often surrounded by the remains of dead civilizations, it's just so beautiful in a sad and haunting way.
Resident Evil 4 and Bioshock also get a mention for mixing the aforementioned feeling with horror elements to great effect, as does Dead Space for its emulation of classic late 70s/early 80s sci-fi horror, and Xenoblade for creating such a great sense of wonder and adventure. (Xenoblade spoilers: The space segment at the end of the game, before the final boss, made my jaw fall THROUGH the floor)








