In Bakuman。, Eiji Nizuma adopts the pen name "Moneys" while drawing Iwase's manga series, so that the editors don't initially find out that he's doing two series at once. This is an anagram of his last name as it is spelled in Japanese ("Ni-Zu-Ma"-> "Ma-Ni-Zu").
Japanese honorifics don't translate well, so Tommy's nameless big brother in Digimon Frontier was named Yutaka in the dub. Tommy thinks of the protagonist, Takuya, as an honorary big brother, and Takuya also has a little brother himself.
In Dragon Ball Z, the name Videl is an anagram of Devil. Videl is the daughter of Mr. Satan (called Hercule in some versions). According to the author, Mr. Satan's first name is "Mark", which is another anagram in Japanese: it's spelt "ma-a-ku", which rearranges to "a-ku-ma" (demon).
In Final Fantasy: Unlimited, villainous adviser Oscha's name is an anagram of "Chaos", perhaps hinting at his true nature.
In the Haruhi Suzumiya tenth novel "The Surprise of Haruhi Suzumiya", there is a new girl named 渡橋泰水 (Yasumi Watahashi). If you rearrange the characters in her name, you get "Watashi wa(ha) Suzumiya" (I am Suzumiya). She is actually a manifestation of Haruhi's subconscious. Alternate Character Reading helps maintain the mystery; 水 is pronounced "mi" in her name, but alone, it is pronounced as "mizu". Koizumi points out that it was so obvious, that they weren't given any hints and were expected to figure it out on their own.
Nanaba in Attack on Titan has a name that anagrams to "banana", which is a fruit.
More than one dodgyHaruhi Suzumiya knockoff has used this to name their thinly disguised characters. For example, the Haruhi (Hahiru) in the live-action "Suzumiya Hahiru no Yuuutsu", and the Mikuru (Kurumi) in the game "M Scramble".
In Jewelpet (2009), Dian disguises himself as a human named Andy (it's off by one letter in the Roman alphabet, but the Japanese one uses the same letters).
Kuromu (Chrome) Dokuro of Reborn! (2004) becomes the emissary of Mukuro Rokudo after he gets locked in Vindice Prison.
During the Doryu arc of Rave Master, Musica realizes that the River Saly belonging to Ogre is actually the Silver Ray, an object he'd been searching for since before the beginning of the series.
