The house featured on Gakuranman has since been known as "The Royal House". Steve Gaynor on the Gone Home developer blog explains:
The house had been abandoned for many years, but had gone undiscovered and remained almost in the same state it was when it was last inhabited. And it was filled with tantalizing and mysterious clues as to who lived there, what happened to them, and why the house had been left to rot.
The relics in the abandoned house showed that a British man had married into a Japanese family. The relics pointed to the pearl trade as well as falling out, culminating in a group portrait with the foreigner cut out with scissors. For the developers of Gone Home, the ruins showed how the sense of mystery—mystery in ordinary lives—deepened the more you shifted through the ruins.
Other sites, such as TokyoTimes, have also been exploring Japan's haikyo—from schools to love hotels. You can also see some of the photos taken by TokyoTimes' Lee Chapman in the above gallery (his images are watermarked).
Gone Home is being developed for PC and should be out next year.
How an Abandoned House in Japan Inspired Gone Home [The Fullbright Company]