Grand Unifying Guesses/Twins and Reincarnations

The following pairs of people are either reincarnations of each other, or are twins that have been separated at birth

 * Faith and Echo/Caroline
 * Emperor Beld and Ganondorf
 * Durza and Ganondorf
 * This implies that Durza was morally good, since he, you know, DIED, and Ganon hasn't yet. Which means that Ganon is more powerful than Durza. So yeah, it turns out that Eragon is evil.
 * Captain Falcon and Ganondorf
 * Ranma (female) and Kasumi
 * Ranma (female) and Hikaru Shidou
 * Ranma (female) and Lina Inverse
 * Laharl and Ash and Almaz
 * Adell and Luke (Tales of the Abyss)
 * Neku and Sora
 * Minato from Persona 3 and the MC from Devil Survivor as well as Naoto, seperated triplets
 * Riku and Sephiroth, not quite sure on the relation but there is some relation
 * Frieza and Mewtwo
 * Zack Fair and Kaien Shiba are clearly the same person
 * Kirika and Kino and Chiko.
 * Ryuk and Disney's Hades.
 * And the Heath Ledger incarnation of the Joker.
 * Watanuki and Itoshiki-sensei
 * Voldemort and Orochimaru
 * And Michael Jackson.
 * David Xanatos and Gendo Ikari
 * Dartz and Light Yagami
 * Light Yagami and Lelouch Lamperouge
 * And Seto Kaiba, unless you believe he is their estranged love child.
 * Batman and Dr. McNinja
 * Eriol Hiiragizawa, Harry Potter, Negi Springfield, Ponder Stibbons, and Tim Hunter
 * Ansem and Akio
 * The God-Emperor of Mankind and Professor Charles Xavier
 * Couldn't they be not reincarnations of each other, but actually the same person?
 * Master Chief and Cloud Strife
 * Rei Ayanami and Cheza. The evidence is here.
 * Jareth and Nakago ("Everything I've done I've done for you, Sarah. I mean Yui. Yui! I mean -- hey, come back here!")
 * Furthermore, Jareth is Graf von Krolock's brother, who was stolen by the goblins as a baby and raised as their own, eventually becoming King. When he tried to reconnect with his brother, there was a massive falling-out between them over their mutual interest in teenage girls named Sarah who were bored and felt unappreciated at home. However, before going back to the Goblin City, Jareth was pleased to see that his personality type and appearance apparently ran in the Krolock bloodline and had extended to his nephew Herbert.
 * The theory of Jareth's connection with Nakago is solidified by Return to Labyrinth. Because of, you know, the art form.
 * Sailor Pluto and Mamoru (Oooold joke)
 * Miles Edgeworth and Edo Phoenix
 * Shinji Ikari and Elric of Melniboné Hideaki Anno IS a huge fan of English-language science fiction and fantasy, and the personalities of these two characters are so similar that Anno must be familiar with Moorcock's work. There are even some odd parallels in the overall plots, if you squint a bit.
 * Alternately, Shinji Ikari and Charlie Brown.
 * These are not mutually exclusive. Cue Elric saying "Good grief!"
 * In the same vein, Misato Katsuragi, Wonderella, and Bangladesh DuPree are all incarnations of the same person in different timelines.
 * Dr. Clayton Forrester and Beakman.
 * Mr. Fantastic and J.R. "Bob" Dobbs.
 * Mr. Fantastic and Dr. Will Magnus, creator of the Metal Men.
 * Xelloss and Lord Varys.
 * Hyatt and Juushiro Ukitake.
 * Scorpius and Psycho Mantis: deformed pale guys dressed in bondage gear who are really good at screwing with your head.
 * While Mao doesn't have the outfit, he probably still counts.
 * Giles and Shepherd
 * 343 Guilty Spark and C-3PO
 * Dr. Gregory House and Dr. Gordon Freeman
 * Dr. House and Dr. Black Jack
 * Kane and Gendo Ikari
 * Ganondorf and Gendo Ikari
 * Roger Smith and Shinji Ikari. Rei's counterpart is Dorthy, Asuka's is Angel, and Big O itself is Eva Unit 01.
 * Integra Hellsing and Catherina Sforza
 * Micheal J Caboose and Homestar Runner
 * Paul McCartney and Jude Feeney.
 * Chuck Norris and Kamina
 * Captain Jack Sparrow and Orihime. Separated at birth, by time, space, and dimensions.
 * Kisuke Urahara and FaustVIII, although the former doesn't have a wife.
 * Megan and Azula.
 * Peter Petrelli and Y: The Last Man and Emo Peter Parker
 * Sylar and Dr. Manhattan, Spock, John Murdock, Dr. House, and Crowley.
 * Aziraphale and Dr. Daniel Jackson
 * Tenth Doctor and Barty Crouch Jr.
 * Spike and Captain John Hart
 * Bester and Chekov
 * Alma and the Witch
 * Gordon Freeman and Isaac Clarke
 * Lt. Harry Callahan, Captain Harald Kleindeinst, Commander Sir Samuel Vimes, and Judge Dredd.
 * Zidane Tribal and Edward Elric, even before the Actor Rule confirmed it
 * Toph Bei Fong and Vita
 * Yuki Sohma and Tadase Hotori
 * Akito Sohma and Ikuto Tsukynomi
 * Bob the Builder and Handy Manny
 * Calvin and Millie
 * Emily and Sally. Come on, we never find out where Emily went off to at the end of the movie, and butterflies are symbolic of reincarnation. It's perfect!
 * And by extension, Victor Van Dort and Jack Skellington
 * The Series 5 Rangers are either the reincarnation of the Quest-Bannon family or Team Leverage.
 * Sora and Sion.
 * Mugen and Jet.
 * 343 Guilty Spark and Wheatley.
 * Fi and G La DOS.

The nameless hero from Hero is the reincarnation of King Leonidas from 300.
Both take a stand against tyrants, both successfully defend themselves against overwhelming odds, and both eventually fall to a Rain of Arrows. It does seem, however, that the two hundred years or so he spent in the Underworld before reincarnating has mellowed Leonidas somewhat, which is why the hero doesn't ever scream, "This! Is! CHINA!!!"
 * The one calligraphist assassin might have gotten some of Leonidas' attitude, even if he shows it in the more "civilized" form of writing giant letters in the sand.
 * The hero in Hero is also a pussy when it comes to Tyranny. That's BAD mellowing.

Son Goku and Captain Carrot are alternate-universe clones.
Both were abandoned at birth and raised by different species, and both are generally amazingly naive about life. And they're both apparently able to make the most depraved, evil people imaginable behave like pure-of-heart idealists through believing in the goodness buried within them. Moreover, both are fully capable of absolutely destroying the few that don't respond to the "I believe in you!" treatment. Plus. there's the whole Kakarott/Carrot thing.
 * While lacking the Raised by Wolves thing (although he did raise a wolf...) RCMP Constable Benton Fraser is another alternate Carrot. See "Due Rimward" by Paul Jamison for further details.

All formidable older gentlemen who wear eyepatches or wide-brimmed hats are Odin in disguise.
At minimum, this includes Big Boss, Nick Fury, and Gandalf - all of whom were active in Odin's areas of interest.