Well, I watched the anime first, and because No.6 has that sort of story I personally find appealing, I enjoyed it to my heart's content. But after reading what I could of the manga and then later finding a novel on it as well and starting on it, I have to say that even though the anime was good, I still think that the art for it could have been a little better managed, as well as sticking to the manga and the novel. It was just slightly different.
Overall, I'd have to say that out of those choices, I enjoyed the manga the most and then the anime, the novel falling into place after those two. But in my opinion, if you like the sci-fi and the slow-progressing story lines then No.6 just might be your next big thing.