Puella Magi Madoka Magica
This thing is to anime what Majora's Mask was to the Zelda series.

Look, I know the cover-art makes it look all super cutsey and girly. It's not. I know the first few episodes are pretty bland and the series itself is only 12 episodes long... but give it a chance. Make it to at least the 3rd episode, thats the one that will make you regret putting it off watching it for 6 months (like I did). This is one of those anime's that was so good it made it hard for me to enjoy other anime afterwards. This is anime is good because despite the premise and art style, it's not at all the typical happy "power of friendship" thing it briefly masquerades as. This anime is a TRADGEDY, in the narrative sense, and so few other anime can pull this off without being all faux-grimdark about it. I'd say watch it for that alone. It's pretty much the definition of a "deconstruction" too, in that it basically takes what's usually a generic'y fairy-tale'ish premise and goes "hey, what if we actually followed everything out to it's LOGICAL conclusion and let the plot play out that way? Happily ever after or not..."

I'm not sure if I'm allowed to post links here, but if it doesn't get removed, this review explains things much better than I can http://thatguywiththeglasses.com/videolinks/ir/jo/jar/36398-madoka-magica

I do recommend watching it subbed though, the English voice actors are pretty awful.
If you live in the United States you can also watch it free and legally through Crackle's service on Xbox Live or their website.

Relish in Chaos:
it does reasonably tackle some things that just may irk at you at certain points (like Edward's constant *spoiler* ).

Not sure if you should maybe spoiler tag that stuff.

Also i can't tell if you're saying you understand but were still irked by it? or if you were just irked by it and don't get why he was having such aversions. So if it's the latter:

Either way, does definitely fit the bill of thought provoking :P

Gabanuka:
One day I'm gonna find another anime to watch.

I loved Cowboy Bebop but I can't find the effort to find another one to watch. All my friend recommends is Naruto and One Piece

Try Samurai Champloo it's made by the same guy that did Cowboy Bebop and if you dont have a problem with blood and slightly confusing plots Baccano! is another good one with an amazing english dub and it's all on youtube i believe.

Dansen:

Casual Shinji:
NGE

I know it's seen as pretentious and full of itself, but I fucking love wrapping my mind around this crazy show and its selfishly screwed up inhabitants. Which is why I found the Rebuild movies not as engaging... They were just too lean on the nitty gritty mind probing.

Also Berserk. The manga, not the anime - I never saw that one, except for the newer movies which were incredibly lame.

As much as I love thinking about both these properties, I also love talking about them.

I actually like the rebuilds, they are a lot better quality and fun to watch. On their own they would be okay but if you look at them as an extension of the original they are great because you can fill in a lot of the blanks with what you already know about the original characters. I believe in the sequel theory and I cant wait for the third one to come to America. From what I hear the third one goes completely off the rails and into uncharted territory.

With the Rebuild movies I think it depends whether you prefer the more positive mindset compared to the nihilistic one of the original show. For me the fact that the show was way more grim meant it backed up the trauma of the characters that much better. The whole "You may be through with the past, but the past is not through with you" aspect, that isn't as easily resolved as it seems to be in the movies.

I still like 'm okay, just for the visuals alone. Gainax on a big budget is freaking candyland.

I saw the third Rebuild movie, and it does indeed go off the rails... right over the shark.

Naruto......no I am NOT joking I am being completely serious T_T
Naruto has allowed me to think about:
1-How far I would go for my friends
2-The meaning of family
3-And how one overcomes hatred.
It's a show that deserves much more credit than what it get's ^_^

.hack//Sign (the rest of them are of varying quality). I appreciate it even more after watching Sword Art Online. See, whereas SAO had some nice animation, the main character was a huge Mary Sue (Marty Stu?), and the story basically exists to show off how cool he is. But you know, whatever, because all the depth that's missing from Sword Art Online is in .hack//Sign, which really gets into various aspects of playing MMORPGs.

Bakemonogatari, but only if you have a small understanding of Japanese, or at least have a good sense of pattern recognition because everything is a pun. Then you have the achronological storytelling, the mythical allusions, and Shaft's not so subtle visual metaphors and euphemisms.

I know lots of anime that makes you think...
why don't breasts really work that way and come in those sizes?

FLCL

While most of the thoughts wind up being "what the F*** is happening!?" it does strike some really good chords (no pun intended) and plays your heartstrings like a guitar (ok, pun totally intended). Its almost like the less it explains and the more it makes huge leaps in logic the more and more you have to think about what all of this chaos means.

No other anime has left me sitting at my computer so utterly satisfied with what I just watched while my mind brimmed with so many questions that I knew would never be answered unless I watched the series again... and again... and again.

Ghost in the Shell. I had to watch the movie and the show twice to understand some of the philosophical stuff.

Legend of The Galactic Heroes is the king of this.

- War is shown from every angle.
- There is no good or evil side.
- The choice between a just Dictatorship or a corrupt Democracy.
- There is no one who is truly evil, just those who will be more forward about their own gains.
- Quotes that make you think such as...

"Someone like me can hold power and make others live or die as he likes. If that isn't a flaw of democracy, then what is?"

"There are few wars between good and evil, most are between one good and another good."

"All heroes have established thrones atop not just their enemies, but a large quantity of allied corpses as well. There are no monarchs with clean hands. Their subordinates also know that."

"The greatest freedom is the freedom not to get involved."

"An army is a tool for violence, and there are two kinds of violence... Violence to control and oppress, and violence as a means of liberation. You know, what we call a national army, is fundamentally the former example. It's a pity, but history doesn't lie. When those in power confront popular opposition, there aren't many examples of the army siding with the people. Far from it. In the past, in country after country, the army itself evolved into a power structure, and came to control the people with violence."

And my personal favourite: "People get more pro-war the further they are from the front lines"

- An amazing classical soundtrack featuring Beethoven, Mahler, Holst, Satie and Stravinsky to name a few.

10/10 show that everybody should watch at least once.

NGE certainly makes me think. Mostly things like "OH MY GOD WHAT THE FUCK IS GOING ON AAAAAAHHHHH!!!"

I'm not much of an anime person, as you can probably tell.

Evangelion is the classic, though it can seem a bit over-hyped because of its age. It does have some really cool themes and characters though.

Mushi Shi, while not really cerebral, makes you think in more of a ponderous way, about humanity and life and all that.

Now and Then, Here and There is fantastic, all about brutality, slavery, government. Again, not really cerebral, but makes you think.

FLCL(Fooly Cooly), is absolutely crazy, and makes you think it its own strange, strange way.

Milk:
Not sure if you're being intellectually dishonest or just dense.

There's no need to be rude.

A better way to word that would be to say that he murdered tens of thousands of criminals in an attempt to create a lawful society. Until that morally repugnant fucktard Near caught him, he was quite successful.

Even if you word it that way, you just said that he murdered tens of thousands of people. Murder is still murder, even when you murder a criminal. It doesn't become lawful execution just because that person robbed a bank.

You want to know how stupid that is? I guarantee that you personally have broken a law at some point. Is it okay for Light to murder you?

They were enemies of the peace. As the manga states worldwide murder and rape crimes had dropped by 70% under Light's direction. Anyone who dares try to ruin that deserves to be stopped.

Are you counting all the people Light killed in your worldwide murder rates?

And now you're just straight up lying. He states his goals pretty much every chapter.

1. Kill criminals.
2. Scare people into not commiting crimes.
3. Create utopia.
4. (towards the end) rule as a god.

You don't see any problem at all with the fourth step? Or, hell, the first? Those goals are selfish and megalomaniacal. I wasn't lying - they don't justify anything Light did. He didn't do it for the good of the world; he did it so he could rule the world, because he's an egotistical jackass.

Any reform agenda that starts with "Kill people" and ends with "Rule the world as a god" is not a very good reform agenda.

Ghost In The Shell: Stand Alone Complex?
What a coincidence!
I was gonna say Ghost in the Shell 2: Innocence.
It really made me think.

That is, it really made me think: "Why the hell are you quoting Milton out of the fucking blue? And now Dante!? There was no incentive whatsoever for you to be spewing a random quote from Dante's Divina Comedia! You are trying too hard movie! Why are you trying so hard!?"

On a more serious note - I guess Cannon Fodder, the third segment of Memories (a trilogy of short films), was one that stuck in my head for quite some time. There isn't really a story going on, it's more of a "day in the life" experience of this fictitious world where everything revolves around war and fighting "the enemy". Except everyone is just living there lives, we never see any violence or a battlefield - and we never even know who the enemy is. It's one of those cute, little masterpieces (all three of them, actually) that has just enough subliminal messages and vague allusions to make you speculate for hours.

Milk:
You support millions being free to be raped and murdered worldwide, I do not.

Annnnd we're done.

You've done a great job of making the Death Note fanbase look like a pack of vigilante psychopaths, Milk.

Too tired to read through four pages of comments, but regardless I'm pretty sure this one has already been mentioned at least once. If not, well then yay for me!

Paranoia Agent

It teaches us the lesson that bad shit happens if you refuse to take responsibility for your own fuck-ups. :P

No love for Tengen Toppa Gurren Lagann here? That series basically built my entire self-confidence. Awesome music, too.

Probably Yu-Gi-Oh and Naruto. I never felt so alive.

Abomination:
Most anime makes me think "Why would you react like that in that given situation? Are you bipolar or incapable of rational thought?" or "What is stopping you from shooting them? They're RIGHT THERE. Stop staring with your mouth open. You can end this right now."

I am the same way, I just can't stand characters like that! They sit around for like five minutes with the bad guy in front of them while they are fully capable of ending the entire charade. Maybe that's a Japanese thing, feeling like you can do something when you wont, I don't know I am not an expert on cultures I am not part of(meaning outside the USA) at all.

OT:

I would whole-heartily recommend:

Full Metal Alchemist: Brotherhood - This series deals with power and when is it enough, or is it ever enough?

Mushishi - Deals with pretty heavy stuff, and each episode is different: like one is how people deal with death while another is about obsessions and addictions, and another (more open-ended) dealt with mortality; but it is presented so well you don't even know they are doing it, really great series

Cowboy Bebop - This series deals with morality and what people are willing to do for themselves and each other, and where to strike that balance

Tengen Toppa Gurren Lagann - The entire series is one giant metaphor for advancement, (spoilers) They start off under the ground believing the surface world doesn't exist; to COLONIZING SPACE! seriously their magic energy is called within the show "evolutionary energy"; and every villain in the show is evil because of their fear of advancement, seriously best commentary on society and civilization ever.

Most of these are short, but they pack a punch that is both memorable and leaves you thinking

JoJo's Bizarre Adventure. It's truly made me think, "How does one walk such a fine line of overwhelming manliness and sheer fabulousness?"

knight steel:
Naruto......no I am NOT joking I am being completely serious T_T
Naruto has allowed me to think about:
1-How far I would go for my friends
2-The meaning of family
3-And how one overcomes hatred.
It's a show that deserves much more credit than what it get's ^_^

The promblem is that after the sasuke and naruto battle of the original the series is bogus; and with shippuden is that it can be very slow at times; but if you can get through all that it does get into the things you stated.

jamesbrown:

knight steel:
Naruto......no I am NOT joking I am being completely serious T_T
Naruto has allowed me to think about:
1-How far I would go for my friends
2-The meaning of family
3-And how one overcomes hatred.
It's a show that deserves much more credit than what it get's ^_^

The promblem is that after the sasuke and naruto battle of the original the series is bogus; and with shippuden is that it can be very slow at times; but if you can get through all that it does get into the things you stated.

While I will admit shippuden is not as good as part one I still feel that it is good mainly for the reasons stated below:

Milk:
Only some. Most of the plebs still prefer to have millions of innocent people raped and murdered.

Fucking deontologists.

I'd respond properly, but you're making a better argument in favour of my point than anything I could come up with.

I noticed that Bakemonogatari has been mentioned but I wanted to put again since I think it's a great anime. Also noticed that Mnemosyne was mentioned, and wanted to give you fair warning before you watched it. Mnemosyne is a grusome anime, bad enough that I don't want to get into details of why I think so but I thought it only fair that you know before watching.

You're in luck OP, "cerebral" anime happens to be one of my favourites! Let's go! Buuuuut it's getting late, so just one recommendation for now!

Kino's Journey - Starting with my top recommendation here. Kino's Journey is the story of a young traveller named Kino. Kino travels by motorbike in a fantasy European-esque setting, going from country to country, staying at each country for no more than three days (Kino explains that three days is enough time to learn what a country is like). Each country that Kino visits usually has some kind of cultural or social theme, which will usually be what the topic of the episode will be. The series covers many different themes, including cannibalism, democracy vs dictatorships, prophecies, the relationship between man and machine, science, religion, traditions, work and war. I find this series to be endlessly fascinating and keeps me thinking about it years after I watched it. Watch this!