There are actually two completely unrelated series both called Gakuen Heaven. One is a Yaoi Guys series set in an all boys school, the other is an ecchi series about a ronin teacher set in an all girls' school. Don't get 'em mixed up.
On a similar note, there are also two series called Gakkou No Sensei. One is about a male teacher at a supernatural school of some sort (I haven't actually read it, so I could be wrong), while the other is about three female teachers who also happen to live together. Adding to the coincidence, they both have hints of Ho Yay (the first one) and Les Yay (the second one).
Non-human example: Both Code Geass and Tengen Toppa Gurren Lagann feature a mecha named 'Gur(r)en', both of which are Red and Very Awesome. (Both are spelled the same way in Japanese, but the latter is officially romanized with a second R.) This is because "guren" means "red lotus" in Japanese. See also: Solf J. Kimblee, the Crimson Alchemist, from Fullmetal Alchemist, who in Japanese is called "Guren no Renkinjutsushi".
Yukari Kamishiro is either the main characters' attention-craved drunken flirt of a teacher in Nogizaka Haruka no Himitsu or one of the haremettes in the Gift series.
Sauzā (サウザー) is the Japanese pronunciation of two different Jump-related villains: Souther the Holy Emperor (aka Thouther, Thouzer), the successor of Nanto Hō-ōken from Fist of the North Star; and Sauzer ("Salza" in Funimation's dub), one of Cooler's henchmen in the fifth Dragon Ball Z movie.
Lampshaded in Haruhi-chan with Kimidori, the (male) artificial lifeform balloon animal, who is totally not Kimidori, the (female) Artificial Human who works with Yuki. That being said, 'Kimidori' means 'yellow-green'. The latter's hair and eyes while the former is a yellow-green balloon animal.
Not exact, but Yukino Miyazawa is a high school student voiced by Atsuko Enomoto. Yukine Miyazawa is a high school student voiced by ... Atsuko Enomoto.
Both Pokémon and Digimon Adventure have characters named Hikari, although the Hikari in Pokémon (introduced in 2006) had her name dubbed as Dawn, while the Digimon Adventure one (introduced in 1999) became Kari.
The main hero in both Dragon Ball and Saiyuki is Son Goku, a Saiyajin/man with a staff. It's because both stories are based upon Journey to the West, whose main character is named "Sun Wukong"note The original Chinese pronounciation of the characters that are used in writing the name.
Robotech's Rick Hunter (AKA: Macross's Hikaru Ichijou) came a couple or so years after the Rick Hunter played by Fred Dryer in the TV show Hunter.
The main character in Ai Ore! Love Me! is named Akira Shiraishi. In Lucky Star, Hiyori points out that it sounds like the Lucky Channel characters Akira Kogami and Minoru Shiraishi got married. (And the doorbell rings, leaving Konata to wonder which one it is...)
Digimon somehow pulled off two internal examples between the same two media - both the manga Digimon Next and the anime Digimon Xros Wars have characters named Yuu and Tsurugi, though in Xros Wars Tsurugi is that particular character's surname as opposed to the Next character's first name.
Hibiki & Kanade are a pair of main characters from a music themed Magical Girl series... well, but whichseries is meant? (Though it's worth noting that one pair of them is an actual duo while the other pair is not since one of them died before the other one became a Magical Girl.)
The Goddess Madoka's best friend has a love interest named Kyousuke, who was also one point of a Love Triangle in the '80s rom-com Kimagure Orange Road—but for this Kyousuke, one of his love interest is also named Madoka.
Two shogi manga, Sangatsu no Lion and Shion No Ou both have supporting characters named Nikaido who are both kishi and affluent due to their families. Aside from that, though, they are as different as night and day.
Elfen Lied has one in-genre example,and one unrelated. Another short manga story called Elfen Lied focuses on two musician prodigies attempting to keep promises they made in childhood - if the plot sounds familiar, it should. The story was written and drawn by Lynn Okamoto, and first published in a manga compilation volume for the series Elfen Lied. It has no connection to the world of Diclonius and such. In Germany, author Bernard Hermann publishes a series about fantasy elves with each title being Elfen and then another word, with one of them being Elfen Lied.