Yeah, Black Lagoon is sort of like it, but it's a more mature story than Cowboy Bebop, mature in that it's dealing with some harsher realities and just in general language. It's been good what I've seen of it so far.

Paranoia Agent is great for what you described Xanatos. Similarly, you would probably enjoy Perfect Blue and Paprika, also by the same director of Paranoia Agent. Perfect Blue I felt was perfectly summed up as if Disney and Hitchcock made a movie together Perfect Blue would be that movie. It's very Hitchcock in story, mystery and pacing. It's not as mind screwy as Paranoia Agent, but it has some really good twists. Paprika is a science fiction thriller of sorts. The best thing about it is the really amazing and trippy visuals, but a solid story and good mystery accompany it.

Hyouka, which I think I mentioned, is specifically a mystery anime. It's focus is on a girl who is crazy curious and has these eyes that suck you in and a boy who is very observant and has excellent deductive skills, but has a life motto of being as a lazy as possible, but more accurately he wants to expend as little energy as possible, which amounts to being lazy and apathetic. It has some really great mysteries and twists which will live you thinking and guessing until the end.

Bakemonogatari, also suggestion, currently is Bakemonogatari, Nisemonogatari, Nekomonogatari (Black), Nekomonogtari (White) and Monogatari, which an eventually Kizumonogatari. It can be simply called Monogatari series, but Bake is the place to start and Monogatari is the place to end, not confusing at all. But it is a series with a heavy focus on trippy, unique visuals, quick snappy dialogue and really entertaining characters. It's often heavy on character interaction. The first series Bake, is great for an opener because main character aside all of the characters he meets have become affected by Japanese gods/spirits which cause problems for them. Specifically the first girl has no weight as a result, she looks the same, but weights nothing. Solving the source of the problem and dealing with it is the core is the issue. And things never turn out as they seem from the start. There's always something revealed that changes the way you look at the character or how they need to be saved. It's a very solid series, but it very unorthodox in presentation and will require lots of pausing, freeze framing and rewinding because they cram tons of supplemental material in. It entertains though.

Steins;Gate is about time travel, but its more about the consequences of when you play with time travel. Without giving away the plot, it starts fairly calm and lighthearted, minus a murder that only the main character seems to remember, and then after playing around with time travel discovers he caused something to happen that he now must undo. And he learns that there's a lot bigger picture than he realized and one twist after another starts connecting the dots in ways he never realized. It's a really great story on time travel with plenty of mystery and twists along the way. I was hooked after the first episode or two.

A little outside of pocket, but Nagi no Asakura is a slice of life story that ends up turning very serious and very dramatic after about 6 episodes. It's got a lot of romance, but a surprise twist in what seems like a light fluffy story will sort of leave you a little shocked for a bit as things go down a completely different road then you expected. It's a very well done romantic story with strong character growth and breathtaking visuals. And prepare for the feels as they call it, because it delivers them in the second half of the series frequently.

Shin Sekai Yori (To the New World), it's got a bit a slow start, but one thing it does in spades is present you with plenty of questions and mysteries. It's a very interesting world that's post-apocalyptic. Something happened that wipes out a significant percentage of the population and in the centuries that followed the survivors remain in villages. Every single human has telekinetic powers of some type. Controlling the powers as a child is the initial focus, but there are dark secrets in the world that become the main focus and the cost of learning said secrets. Probably the most unusual thing that did end up turning off some people watching it is that the society encourage intimate same sex relationships to all of the teenagers, like 10-14 or something. It's meant to be encouraged as a way to calm them in stressful situations and discourage violence. They naturally then are encouraged out of it once they start seeing the opposite sex as attractive. Needless to say, the anime does show two boys making out and two girls making out and that ended up offending some. Still it's a very good anime, sometimes a little slow, but when it goes going it won't let go of you.

Danganronpa is a straight murder mystery based on the game of the same name. The setup, 12(?) high schools are brought to a school where it is completely barred and locked in. Then are informed the only way to escape is to kill one of the other students and get away with it. When a student dies, the rest has a period of time to investigate for clues to figure out who did it before presenting their evidence and accusing someone. If they are correct the murderer is executed, if they are wrong everyone that's not the murderer is executed and the murderer is given freedom. Strange characters and things are never as they seem, you'll get plenty of your mystery and twist.

Gargantia on the Verdurous Planet comes from the creator of Madoka, mentioned above. It's a mecha story about a boy that is in a strange land. He pilots a state of the art combat mecha that during a retreat from battle sucked him through a wormhole and dropped him off on the planet. It's sort of like Waterworld, the planet he's left on. Land seems non-existent as everyone lives on boats and the former civilization is submerged under the oceans. The people have a very different lifestyle from the boy who only knows how to be a soldier. So it's a classic fish out of water or dances with wolves type, but it comes from the man that did Madoka, so you can expect twists and mysteries. It takes longer to reach than Madoka, but the payoff is worth it. It has fun likeable characters.

Ghost in the Shell and specifically Stand Alone Complex and 2nd Gig, if you like cyberpunk the original Ghost in the Shell movie was many young anime fans first introduction to the world of cyberpunk. At it's core it is a police story, but your cops happen to be cybernetically enhance, have superhuman strength or other attributes. There is a heavy focus on the net, what it means to be human and what is a soul and do you have to have a human body or even a body to still be human. Stand Alone Complex has stand alone episodes and arc episodes. It can be hard to follow tossing out both Japanese names, political maneuvering and literature quotes it can be enough to make your head spin. But it has action, adult mature characters and story with some good detective mysteries and twists. It's heavy on politics.

Little Busters and Refrain, if you watch Little Busters, Refrain is required viewing or you won't know how it ends. It comes the same people that did the above mentioned Angel Beats and based on a PC visual novel. It seems like your run of the mill slice of life high school anime, but it's not. The first series will provide you no answers and only questions. Nothing is explained, even though the whole thing is working on a very specific set of rules, they never tell you the rules. Which is actually important because if they did, it'd ruin the twist and it is a big one. Oh and the feels are strong in this one too, really strong. This is a story about the characters, their history and their relationships and friendships with one another. I can understand people staying it's too long of a wait for the payoff, but it is a good one, it just takes a while to get there. If you can get invested in the characters, it'll care you to the end.

Last Exile has a very interesting world that drew me in. It has a pre-WWI European etiquette that was interesting. It's basically about a Captain Ahab type character, but you don't really know what the whale is that he's hunting. It's just very clear he's a man on a mission. The story focus on two kids that love to fly their later fathers vanship (a steam-like powered personal airship). They are message runners and on their off time race. They love the sky and flying more than anything else. They end up caught up in the world of this man on a mission and start to peel back the layers on the world. Really strong and interesting characters, lots of passion and driven personalities with some really cool designs and interesting world construction. There' s a sequel out for it, I've yet to see it.

ROD the TV, is the follow up to R.O.D. a movie, which Read of Die. Like the main character of the movie, the main characters (3 sisters) have a special power that allows them to control and manipulate paper to do anything like barriers, swords, dolls, whatever they want they can even make it stop bullets. Both are great watches, but the TV series picks up after the movie where the main character is missing and a friend/author of her ends up getting the sisters as bodyguards. Discovering their powers, she wants them to help her find her missing friend. Which ends up being a much deeper matter than they thought with conspiracies, betrayals and plenty of good action all around paper and this woman the author which is actually targeted for a surprising reason.

Rah Xephon, I call it Evangelion lite, if Evangelion is not something you can stomach because the main character is too splineless or angsty, Rah Xephon is less of that. The character is a little more competent. But it is still the cast of "alien-like" forces are attacking humanity and humanity has something that is able to fight them off that's very similar to the alien. There's a lot of unknowns early on and plenty of reveals as things go on. A far bit of the global conspiracy and large players at work manipulating things.

Bynrhild in the Darkness comes from the creator of Elfen Lied. It's a bit haremy, but it's good because the main character is competent and has great deductive skills. While not out right mysteries, he's trying to protect a group of girls that are being hunted down to be killed. One girl has foresight, but only sees an image and they must interpret it with what she can provide. So there is a good amount of solving the problem and coming up with a solution. There's some good twists that come along, but expect a lot of deaths. It's still currently airing, but will be finished by July. If you enjoyed Elfen Lied, it's a more sane and less extreme version, but no else grim or dark, considering it's dealing with girls being hunted down to be killed and they have a time limit on their life, which if allowed to pass their bodies break down on the molecular level. So there'll be lots of blood.

That's the initial list of things I could think of from the over 500 anime I've seen. Let me know if you want to know more about a specific one.