I don't remember who posted it right now, but there are a few threads on the 999 Gamefaqs board with recommendations. :) Aside from that though, you definitely need to play (read) "Ever17 -the out of infinity-" as it was written by the same man (Ushikoshi) who wrote 999. Not to mention, it has one of the best stories in ANY form of media ever, not just video games or books (seriously, Ever17 easily ranks among some of the greatest stories ever told). It's a visual novel (basically a book with pictures, music, voices, and event scenes) like 999, but without the puzzles. You can download the full English version on ErogeDownload. :) The story is about 7 individuals trapped in a high-tech underwater amusement park. That's all I can really say about the plot- anything and everthing else is a spoiler, pretty much- but I highly, highly recommend it! It's one of my favorite stories of all time.
Haha wow is it really written by the same guy? No wonder it reminded me of Ever17. As for the OP, I agree with the recommendation for Ever17 as well, just keep in mind you'll have to be a bit more patient with it. It is definitely worth it though.
It's been several months since the original message, so I would assume the OP has already either played ever 17, or not... but for anyone ELSE reading now or in any divergent-river-future timelines ;) - I agree with both recommendations above for ever 17. It ranks as (for me) THE single most mind-blowingly awesome and amazing story in any game, I've played, ever. I know that may seem like a lot of superlative hype, but I can say without hesitation or doubt that my review here on Amazon for ever 17 from 6+ years ago is STILL true to this day: nothing compares to it, except (as of this weekend when I finally finished it...) 9-9-9, which came close.
Put simply - if you played through to the True Ending of 9-9-9 and enjoyed the final core story, themes, and the blend of science, mysticism, fantasy, and affecting destiny... then ever 17 will absolutely fit the same bill. It's older and more a visual novel (i.e. no puzzles, just branching choices), but the story, characters, and the "oh...holy...WOW!" moment are all absolutely top-notch.
I may have to re-play ever 17 over the next couple of weeks, while waiting for Virtue's Last Reward to come out, actually :)