999 is a very interesting game that I only completed earlier this year myself. I can recommend it to any fan of visual novels and locked room puzzles, and seeing it's just been released on the Japan iOS store with an English port coming in Quarter 4, it will be much easier for those who wish to play it to do so.
Here's the thing though, they've removed the locked room puzzles to focus more heavily on the visual novel aspects. To this end they've created a more comic book style presentation, and a flowchart system similar to the one in the game's sequel Virtue's Last Reward (which I shall be playing whenever I finally grab a 3DS).
For those unfamiliar with the game, here's the trailer from the original DS release. It doesn't tell you much, but it might get you interested. 999 is certainly a story worth experiencing.