After the apocalypse in Final Fantasy VI, Edgar works incognito as the bandit chief "Gerad". Oddly, he does this even if you change his name to something other than the default.
Aerith's name anagrams to "I, Earth", though it's obscured by the fact that the English localisation romanised her name as "Aeris".
Aerith's late mother was named Ifalna, which is an almost-anagram of "final", not only referencing the series but also the fact that she was the last full-blooded Cetra.
In Final Fantasy VIII, the song "Fithos Lusec Wecos Vinosec" is an anagram for "Love" and "Succession of Witches" (two of the game's major themes.)
The names of the members of Organization XIII are anagrams of their original names — or in one case, a name they stole from someone else — with an X added in. Of particular note, Xion, the "14th member", is No. i, as in the imaginary number.
Xehanort's name is an anagram-plus-X of both "another" and "no heart". "No Heart" is used as the name of a Superboss in Birth by Sleep Final Mix: Xehanort's Keyblade Armor.
"Ansem" can be rearranged into "Names", which is oddly appropriate given the amount of people who've called themselves that.
Eraqus is an anagram of Square, one of the series' developers. This is to parallel Yen Sid, which as noted in the Western Animation section is Disney backwards.
Bragi from Kingdom Hearts Dark Road is an anagram of Braig, Xigbar's human self. As it turns out, they're both vessels of the ancient Keyblade Master Luxu.
In Escape Velocity: Override, the three alien races/cultures known as the Strands are named Azdgari, Zidagar and Igadzra, and there's a planet known as Gadzair. Word of God says that the Strands are all the same species (this part is in the manual) and Gadzair is their homeworld (this isn't); this isn't actually part of any plots but was added as a plot hook for mods and future sequels.
Much has been made by fans over the possible relationship between new character Mender Silos and established villain Lord Nemesis. Whether or not this is significant has yet to be revealed, and it may just be a red herring. Of course, "Mender Silos" came into the game shortly after "The Honoree", which was a Paper Thin Codename for backstory character Hero-1. The City of Heroes staff do love their Significant Anagrams.
Issue 19 of City of Heroes confirms that Mender Silos is a future version of Lord Nemesis.
The City of Villains respec trial contacts are named Sparcetriel, Trepsarciel, and Ractespriel.
In Baldur's Gate II, the famous Dungeons & Dragons character Elminster may appear to speak to one of the party. When doing so, he uses the rather transparent anagram "Terminsel".
The main villain is a man named Stauf, who apparently came by his riches and success via a deal with the devil. If this isn't clear enough, one of the puzzles in the series involves rearranging trains to spell his name. They are initially positioned to spell Faust.
Another puzzle also qualifies as a Significant Anagram; the player is presented with a Tic-Tac-Toe-like board on which Scrabblesque tiles are arranged. The letters must be rearranged to spell three words, one in each row. The words are GET BOY TAD, which gives the player some idea of what Stauf wants from his guests and how the game is going to end.
And another puzzle earlier on involves rearranging the cans in a pantry so that their labels spell out a sentence, which foreshadows later events in the game. The catch is that the only vowel provided is 'Y'. The solution is "Shy gypsy slyly spryly tryst by my crypt".
In Apollo Justice: Ace Attorney, Kristoph's name in the Japanese version is Kirihito, an anagram of 'hitokiri', meaning 'killer'.
Earlier in the series, the founding member of the Fey spiritualist clan is Mystic Ami. This name was chosen in the English version because it anagrams to another phrase, "I AM", which, aside from being grounds for the localization to be struck by the Judeo-Christian God, is relevant in a certain case. By possible coincidence, it also anagrams to "Mia", one of Ami's descendants.
And in Case 3 of Ace Attorney Investigations: Miles Edgeworth, "Oliver Deacon" turns out to be an alias of Colin Devorae, the secretary who was forced into Taking the Heat for the Amano group, and his Japanese assumed name is also an anagram of his real one.
Super Robot Wars Z introduces a character named Asakim Dowen, who's essentially an Evil Counterpart to the franchise's first Original Generation character, Masaki Ando. His name anagrams out as "Masaki Endow", a nod to JAM Project singer Masaki Endou, for whom the character Masaki was named.
Ancient Domains of Mystery uses these for a number of names; Tywat Pare from Wyatt Earp, Lawenilothel from hole-in-the-wall, Gaab'Baay from Baba Yaga, and the fourteen statues in the Bug-Infested Temple which are named after Thomas Biskup and the thirteen prerelease testers.
Few fans ever notice it, but "Tauren", a player character race who loves the outdoors, is an anagram of "nature".
Players meet Matthias Lehner, who turns out to be Arthas Menethil. Or at least, the last remnant of his humanity.
In a more comedic than significant example, there's the group known as D.E.H.T.A.— Druids for the Ethical and Humane Treatment of Animals. Rearranging a few letters gives you "D.E.A.T.H." (they send you out to hunt poachers for their ears).
And another funny example, a boss in Naxxramas, one of the raid instances in WoW, is named Loatheb. He's known for having an ability that makes it impossible to heal for most of the time you're fighting him. His name's an anagram of Healbot.
In one questline, Sylvanas Windrunner masquerades as Lindsay Ravensun. It's a flawed anagram, but "Lindsay W.N.R. Ravensun" would have been rather suspicious.
In the End Time instance there's the leader of the infinite dragonflight Murozond, an anagram of his uncorrupted past self Nozdormu, leader of the bronze dragonflight.
Seer Hao Pham Roo in Mists of Pandaria patch 5.3 is Emperor Shaohao, the emperor from ten-thousand years ago.
Alan Probe, the star of Amateur Surgeon. Just switch two letters in his first name and you have "anal probe". Which... sort of has something to do with medicine.
The Wand of Nagamarnote an anagram of anagram is required to defeat the main boss without exploiting the kind of loophole that tends to get immediately closed after use. This is something of a Guide Dang It! moment.
The December 2009 event involved a newspaper. Almost all of the newspaper's bylines are anagrams of "Mr. Skullhead", the member of the devteam who was in charge of that part of the event.
Rene C. Corman, the name of the villain behind the 2010 Halloween event and 'The Skies over Valhalla', is an anagram of Necromancer.
Dr. Chakwas of Mass Effect, whose name is an anagram of "hacksaw." According to Word of God, it's meant to play off "sawbones" as a nickname for a trauma surgeon.
The Legend of Zelda: The Wind Waker: Tetra's Italian name is "Dazel". Now switch around the letters and see what you get. The weird thing is that this painfully obvious anagram actually sounds a lot better as a name than her real, original Japanese name...
In Star* Soldier, the manual for Wing Commander Arena, one of the entries in the timeline lists a "Rein Etorbs" as an author of a book series The Darkening. Erin Roberts (brother of Chris, the WC creator) was in charge of what eventually became Privateer 2: The Darkening (originally just "The Darkening" before Executive Meddling).
In the Inferno campaign of Heroes of Might and Magic 5 you play as a Noble Demon general Agrael. In the subsequent League of Shadows (dark elves) campaign you play as an aspiring dark horse warlock named Raelag. Then there's The Reveal. Players recognized the Agrael/Raelag anagram, effectively spoiling the surprise before the game came out.
Just Cause 2 has the arms dealer Sloth Demon. Players can use this trope to figure out he's actually Tom Sheldon.
The Interactive Fiction game Delightful Wallpaper, intended as an homage to Edward Gorey, was submitted by author Andrew Plotkin under the anagram "Edgar O. Weyrd".
Runescape has a mahjarrat named Wahisietel who hasn't been seen in decades. There's also a strange man named Ali the Wise who seems to be an expert on the mahjarrat. Hmmm...
In the Alternate Reality Game for Batman: Arkham Asylum you agree to help a woman named Wendi Maga, who claims to have a doctorate in psychiatry, hack into the Arkham security system. Dr. Wendi Maga anagrams to Edward Nigma.
Mareep (which resembles an electric sheep) actually gets its name from an anagram of the word "ampere", which is used to describe the intensity of an electric current.
Dark-type trainer Karen of the Johto Elite Four's name is an anagram of "darken" without the D at the beginning.
Dunsparce's Japanese name, ノコッチ (Nokotchi), is an anagram of ツチノコ (Tsuchinoko), the cryptid it's based on.
Ice-type Eeveelution Glaceon’s name anagrams to “congeal” (to freeze).
The lobster-like Clawitzer's Japanese name, ブロスター (Burosutaa), is an anagram of ロブスター (Robusutaa), meaning "lobster."
Safe Cracker has a jukebox listing 12 real-life song titles, with other meaningless titles around them. The player is supposed to figure out which artists made the real ones (which you can find out elsewhere in the Crabb house), unscramble the fake songs and select them in sequence with the real ones. "Stab the eel", for instance, translates to "The Beatles".
In the first dream world of Obsidian, your initial objective is to find a document that can fix the Broken Bridge to the chief's office. It's filed under a two-word title, but every document in the archives is listed as single words. The trick is to play an anagram game on the archive computers that can create the longest possible word from two given words. Standard Damage is revealed to be Tradesman.
The title-giving Lost Superweapon of the Interactive Fiction game The Weapon is called the Yi-Lono-Mordel. This is an anagram for the term "One Room Dilly", which is a nickname for one-room Interactive Fiction games. This hints that the game takes place all in one room, but the Yi-Lono-Mordel itself is far bigger than just the room.
Danganronpa 2: Goodbye Despair has Nagito Komaeda, whose name is mostly an anagram of Makoto Naegi, the first game's protagonist. No, they're not the same person, but Komaeda can be seen as an Evil Counterpart to Naegi. Incidentally, the part that's unused is "Da", a less-polite form of "Desu", roughly translating as "Is" or "Am." Keep in mind that Japanese normally doesn't use pronouns and merely implies them.
An anagram is the solution to one of the puzzles in Mystery Case Files: The 13th Skull, and also a significant clue to the backstory of the game. Two different characters have names which are anagrams of one another - they're really the same person.
Professor Layton and the Azran Legacy: One of the regions Layton and his friends have to visit in order to gather the Azran eggs is Mosinnia, where a mysterious event has caused all adults to fall asleep indefinitely. After the mystery behind the event is solved, the adults wake up, but since many of them had fallen asleep for a whole week, they're having a difficult time sleeping once again. Tellingly, the name of the town is an anagram for insomnia.
Tekken: Kazuya is an anagram of Yakuza, which is what the Mishima Conglomerate was supposed to be a front for. This is confirmed by the game's creator.
One character in The Lost Crown uses the surname "Spitmoor" as a hint that he's not whom he claims he is, as it's an anagram for "impostor". Its significance is somewhat obscured by the fact that "imposter" is just as valid a spelling for the word it converts to as "impostor".
Dragon Age: Inquisition has a subtle, but extremely important one hidden in the name of Solas' personal quest "All New, Faded For Her". When the letters are rearranged, they read as "Fen'Harel, Dread Wolf". One guess as to what's revealed in The Stinger.
In Bravely Default, Spell Fencer Ciggma Khint's name is an anagram of "Magic Knight". This is also true of his Japanese name: rearrange the katakana in "Ikuma Najitto" (イクマ・ナジット) and you get "Majikku Naito" (マジック・ナイト).
In Aion, you eventually learn that the leader of the revolutionaries, Lephar, is Israphel.
The antagonist of BioShock is named And(rew) Ryan. The game is basically a deconstruction of Ayn Rand's philosophy.
Asgore Dreemurr is "sage or murderer", while his son, Asriel Dreemurr, is an anagram for "serial murderer", which doesn't describe Asriel himself at all, but fits his Came Back Wrong alter ego Flowey to a T.
The crest of the Dreemurr family, which symbolizes a prophecy foretelling the events of the game, is called the "Delta Rune", an anagram of the game's title and the name of the spinoff/sequel.
Kris' name is a partial anagram of Frisk, the true name of the player character in Undertale, and a complete anagram of "risk," which ties in with both their status as the protagonist and the endings of Chapters 1 and 2, where they tear the SOUL out to engage in various ominous shenanigans.
Susie is an anagram for "issue". She's got issues. But compared to Kris and Ralsei, this is more mysterious in authorial intent than theirs.
Ralsei is an anagram of Asriel, which foreshadows the reveal at the end of Chapter 1 that he bears a physical resemblance to Asriel under his hat.
Dishonored 2: Meagan Foster's alleged boat is named the "Dreadful Wale". She's already been asked why there's no "H" in "Wale". That's because it's an anagram to "Farewell Daud", which is a hint that she's definitely Billie Lurk, Daud's former apprentice.
The dub of Inazuma ElevenGO has the leader of Fifth Sector, Alex Zabel. It's an anagram for Axel Blaze.
"Two milkmen go comedy" = "Welcome to my kingdom." Zero's greeting to the players, which connects with Zero III's proclamation of being the "King of this kingdom". Possibly unintended, but the "Two milkmen" part might also refer to two players of the Ambidex Game, Sigma Klim and K/Kyle Klim. "Two Klim men".
"Memento Mori, if the nineth lion ate the sun" = "The man on the moon rules the infinite time". The man on the moon refers to Sigma, and infinite time refers to sending his consciousness back decades into the past. Memento Mori when the nineth lion ate the sun also acts in itself as the key for Sigma to pull from the login and password from other timelines when the ninth lion he's seen so far is eating a sun on the login screen. Phi also brings up the intentional typo in "nineth", where the extra "e" was needed to make the anagram work.
"Let's inhibit the virus" = "The truth is invisible." There is another participant who is hidden from the player.
"Let the game end where I treat two" = "Together with me, Delta, we are ten".
"When a curious hate oozes calamity" = "What you choose can materialize us". Certain choices lead to the birth of Phi and Delta.
The game's title itself can be rearranged to spell "Me? I'm Zero, I'm Delta."
While exploring the Shrouded Moors in Diablo III, you encounter a traveller named Daivin, who forces his way into your party and later appears to be killed during a ritual by some cultists. At the end of the temple, Daivin reveals that he's the cult leader, and that he's actually a demon in disguise... his true name is Vidian, Lord of Envy.
In Catherine, Trisha's name is revealed to be an anagram of Ishtar, alluding to her role as the mastermind of the story as the goddess of fertility and love.
The name of Kirby and the Forgotten Land'sBig Good, Elfilin, is an anagram of "Nil Life", hinting at his nature as the kindness and compassion within Fecto Elfilis, an Omnicidal Maniac, given form. It should be noted that, in Japanese, Chinese and Korean, Elfilin is named Efillin, which is a Sdrawkcab Name
Gamma Zee, an obscure Macintosh shareware game, is an anagram for "Maze Game".