Trigun, but in particular episode 17. There's a very real debate between pacifists and those who see war as necessary to serve the greater good. A lot of Trigun is basically just reiterating the same dilemma over and over, but episode 17 really sums it up and can even stand alone.

Honestly, to a limited degree, I agree with Knives.

FLCL has alot of great points about wanting to be a grown up, and growing up. A couple of things that come to mind, like how Naota doesn't like sour stuff, or the fact that he uses his brother as a template for what a adult should be. He follows it so much that he carries around a baseball bat and hangs out with his brother's former girlfriend. Also, the fact that he thinks his pops, grandpop, and teacher as all immature.

Yes FLCL is a very whack series. (get it? lol)

When I watched it back in high school, I thought I was so smart being able to figure out all the sexual innuendos.

Code Geass - it's death note but 500x better.

It deals with the simple question of statism and what each general solution to statism in the academic world would entail. That, and there's a lot of similarities to things like Paradise Lost, etc.

eww no, that manga is beyond human's normal mentality. I honestly read it very fast so that I could skip all these brutal slaughters, man, it is one of the most graphically sadistic manga in history. This manga makes MPD psycho looked like childish. ._.

related to the topic, typical anime fanboy would usually answer if Evangelion is one of the most provoking anime they ever seen. 20th century boys is also a very thought provoking series, because it portrayed how man could be so easily believe what they call modern messiah.

Code geass is also worth to mention because unique portrayal of the protagonist, the series makes it hard to see something only by black or white.

But MPD Psycho - much like Gantz, Berserk, Fist of the North Star, Elfen Lied and ilk - IS childish. Or should we say immature in this case, to differentiate between adult and mature content.

As for me, I generally like the thinking man's anime. I wouldn't consider myself high-brow, but a show that makes you think as well as entertained is all good in my books.

Mamoru Oshii's works (Patlabor, Cerberos, Ghost in the Shell movies) make you ponder and question, but they're perhaps not "thought-provoking" in the same sense as most of the titles mentioned (though the term seems to be used very generously here).

I suppose the most traditionally thought-provoking anime I've enjoyed were Haibane Renmei, Ghost in the Shell and Evangelion. All raised questions about varied and difficult issues, as well as required you to think and question what was shown. Haibane on the purposes of life and companionship, issues of suicide and redemption, Ghost in the Shell on the concept of the soul, what defines us as humans, Evangelion on the.. well, it was either about religion or Hideaki Anno's frustrations at society :edgartpg:

My list
Eureka seveN - A lot about war and how it affects people, but also a look at our environment and how we destory it and maniuplate it how we want
Monster - made my brain hurt :p

Kino's Journey. It's a sometimes frustrating, sometimes uplifting, sometimes depressing look at the many aspects of human nature. That show alternately made me glad to be human and ashamed to be human.
Fullmetal Alchemist. A coming of age story, I guess, but with bigger implications about moving on and the value of life.
And I totally second Haibane Renmei.

I really enjoyed 'Now and Then, Here and There'. The start of the first episode of this 13 episode series threw me off into thinking it was another light-hearted otaku show that didn't take itself very seriously. Boy was I wrong. This series delineates the horrors of war, set against a post-apocalyptic backdrop, in which child soldiers are merely tools to be used by hell-bent dictator (that sums most of it up). For a 13 episode series, the show does a great job of developing most of the characters, with great back story. The music in the series, composed by Taku Iwasaki (Rurouni Kenshin Trust & Betrayal OVA) is nothing short of outstanding, and really adds a great deal to some of the more heart-wrenching scenes of hope/sadness/torture in the series. I rate this show as one of my favourite anime's of all time, because it stuck with me, like how Grave of the Fireflies and the Kenshin OVAs did.

I recently started watching Planetes and have really started to enjoy the series. The scenarios' presented are very plausible ones which reflect a lot of controversial future issues that humanity might face. I'll post up impressions on this one when i see it all, but so far it's been great.

Indeed, Berserk is a great anime(+manga) dealing with important topics such as "war", "justice" and "vengeance".
And if you take a deeper look inside, you'll find even more serious thought-provoking subjects.
I hope that the animation studios could release a second part (from the manga) very soon.