If you liked
Boys Be...
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...then you might like
Kimi to Boku.
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Both series revolve mainly around high school life of a close group of male friends. Rather slow paced and episodic, both are heartwarming stories. The narration style is similar as well. Though Boys Be focuses on romance and has some mild ecchi hints here and there, while the protagonists of Kimi to Boku for the most part just muse about little things happening every day -- it is more about the friends' bonds with each other and not with female characters. (It has romance, but right now it's a background element rather than the main focus). There is a big time gap between when these two series were made, but I enjoyed both.
If you liked
Majin Tantei Nougami Neuro
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...then you might like
Un-Go
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The central characters in both of these anime are a detective (albeit forced in MTTN's case) and his/her supernatural slightly creepy "assistant" with unusual abilities. Both assistant characters seem to have a kind of hunger for solving mysteries, though not literal hunger in Un-Go's case. Both anime are episodic mystery stories with a twisted premise. MTTN has an active element of (dark) humor though while Un-Go appears to be more serious.
If you liked
Ookami to Koushinryou
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...then you might like
Gosick
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They are both set as a traveling adventure in old Europe. The relationship between the main 'couples' are very similar, especially in the way the female lead treats the male lead. Both have a fair share of comedy and drama, Gosick is more tragic though (unexpectedly, considering Spice and Wolf feels more mature overall).
If you liked
Yu☆Gi☆Oh!
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...then you might like
Phi Brain: Kami no Puzzle
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The main characters love puzzles and are challenged by different people in an episodic fashion. In both series, the protagonist receives an ancient artifact that in a way takes over their mind and solves the puzzle for them (not so much in Kami no Puzzle as the artifact awakens the boy's true power, whereas Yugi actually becomes possessed by the spirit). In both series, the characters risk their lives in solving puzzles. It also has a mention of Egypt and pyramids and how the puzzles began there, which is another factor present in both. I would also recommend YGO Duel Monsters (original Japanese of course) as it has the theme of protagonists being lured into some shady competition against their will. But all in all, this first YGO series is more similar to Kami no Puzzle (and also focuses on various games, unlike Duel Monsters which focuses on just that), though certainly has a much darker and creepier atmosphere.
If you liked
Petshop of Horrors
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...then you might like
Kyuuketsuhime Miyu (TV)
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Both of these anime are composed of independent horror stories involving the supernatural, and are both aimed at female audience. But what makes them really similar is the meaning behind the concept. They both portray the dark side of a human heart, and the idea that more often people lead themselves toward their own demise. The dark and gloomy atmosphere, and the overall feeling, is also present in both.
If you liked
Gungrave
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...then you might like
Heat Guy J
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Both explore themes of close friendship and betrayal. Both involve mafia and police; both have sci-fi elements. Both are serious realistic dramas with introspection and great character development, but Gungrave is much more tragic.
If you liked
Aru Tabibito no Nikki
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...then you might like
Tsumiki no Ie
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They have a similar art style and color theme. Both are accompanied by music and lack dialogue. Both are surreal and mysterious; and share a calming and somewhat bittersweet atmosphere. Also, both focus on only one central character, and the world through that character's eyes.
If you liked
Keroro Gunsou
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...then you might like
Gintama
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Gintama and Keroro are both very random and very funny. They also share similar parody elements and break the fourth wall all the time. Both have a lot of interesting characters and are episodic for the most part. And of course, both are fun to watch :D
If you liked
Good Morning Call
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...then you might like
Tokyo Marble Chocolate
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Both are short and simple, but very touching love stories. :)
If you liked
Tactics
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...then you might like
Matantei Loki Ragnarok
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Tactics and Loki are both mystery stories that deal with supernatural beings (or 'occult detective' stories, if you prefer), and are based on mythology/folklore (Norse in Loki's case, and Japanese in Tactics' case). They are episodic for the most part, with the main plot emerging in the second half of the series and toward the end. On the surface, they are both seemingly comedies, but there is also a lot of drama as they touch upon the relationships between people. The overall feeling these two anime give is very similar. You can even draw connections between some of the characters. Aside from that, Tactics and Loki are also based on the manga by the same mangaka, animated by the same studio, and directed by the same person. And both are epic... >.>
If you liked
Hunter x Hunter
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...then you might like
Rekka no Honoo
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Both anime involve a group of friends traveling together and engaging in independent fights, as well as tournament-style fights. They are both great series, especially for martial arts lovers. Both have interesting characters, each with their purpose for fighting, a mysterious group of antagonists, and a lot of fun to watch.
If you liked
Loveless
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...then you might like
Earthian
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Both Earthian and Loveless stories are from the wonderful mangaka Kouga Yun. Both are unique and beautiful and portray an image of somewhat melancholic romantic relationships between boys. Other than that, the stories are completely different, but are both worth watching (and especially reading, since the anime shows only a portion of the whole story in both cases).