First, some comments on some of the series that have already been recommended. (:
Ender's Game: Oh yeah, this series is absolutely amazing. It's been so long since I read the series, but I remember how the complexity and depth of the characters is just phenomenal, and the world Card constructs is one of the most believable I've read in terms of space travel/alien encounters type of stuff. The series deals with such topics as war and religion in a subtle way, and often surprises you when you've just come to believe that the books are promoting a certain message by turning around and demonstrating a much deeper and more complex view of the situation. I think I've read fewer series I admire more than this one. (I really need to get back and read these again, I've only read the first of the new prequel books on the leadup to the war with the Formics. I know at least one more has come out since I read that one.)
Percy Jackson: I didn't read this series until recently (it was on the recommendation of AF fans here on this forum I finally picked it up, hehe), and it's definitely a ton of fun. A broad cast of interesting characters, and you really learn a lot of the more obscure legends surrounding the Greek gods. I enjoyed all the books, but personally, I definitely got more into it with the sequel series, The Heros of Olympus. The introduction of the Roman camp, and the new characters (I loved the start of the first book, meeting Jason, who doesn't know who he is or what's going on, and Piper and Leo), plus seeing Percy, Annabeth, Nico, and all the others a little older was awesome. I don't know what it is, but I really love seeing series that can capture a broader sense of time, starting out with kids as the main characters and getting to see them get older and change over time. (That's part of the reason I love Harry Potter so much, and Artemis Fowl has that too, to an extent.)
Oh, there's also another series Riordan wrote about demigods, only the story revolves around the Egyptian gods instead, which I've been wanting to read. (I read the first book, and from what I've read, it seems the two stories coexist in the same story universe, and I think there's even a short story where the two stories intersect. I really like seeing stuff like that.)
The Queen's Thief series (including The Queen of Atolia, etc.): Someone recommended this one to me awhile back, and it's really good. The story is crafted in such a clever way, you almost can't believe the twists this story takes. (Not sure if I've read the latest one that's out, I really need to check it out. I've fallen behind on so many series. X3)
Another series I'd recommend, Pendragon by DJ Machale.
This is a series I picked up in junior high, and read all the way through the end. It's been a long time since I read it, but looking back I'd say it has a similar vibe to the Percy Jackson series, with a lot of humor, a lot of action, and powerful moments of real drama. It creates a very interesting larger world, which you learn about and discover a bit more book by book.
As for my favorite book/series besides Artemis Fowl...Probably have to go with Animorphs. They were my absolutely favorite books back when I was in second grade or so (probably up through sixth grade, before I got onto Yugioh X3), and a couple of years ago, I decided I would go through and read the entire series beginning to end again. I was floored by just how good the series was, especially in deeper aspects of the story that, as a kid, I didn't really pick up on. The characters are both iconic/memorable, but also complex and nuanced, and the mix of humor and drama is incredibly well done. It's like Harry Potter and Artemis Fowl in that the target audience is kids, but there's a lot of deeper themes going on, and I particularly found it's commentary on morality in war and how war changes people (in the context of this secret war with aliens) very striking. The series also builds up quite a diverse and fascinating set of different aliens, capturing at once very particular cultures of each race, but also creating believable individual people within those races. I absolutely love this series.
“After all, absolutely no one can help but suspect a criminal, liar, and manipulator of committing crimes, lying, and manipulating. And of course, no one is more aware of that simple fact than Artemis Fowl.”
Opal sets into motion her most diabolical scheme yet, to frame Artemis and turn his closest friends against him. Only this time she has a new calculating partner who knows Artemis better than he knows himself. [An Artemis Fowl fanfiction, set after The Atlantic Complex.]
...Shameless self-advertising, guys! C;
(And if you're really bored: AF fanart. ;J)