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).
There's a group of people called "Fairy Tail", but are they a Chaotic Good group of magic users or a Chaotic Evil gang of monster terrorists?
The Pokémon Ledian and the Gundam Wing character Lady Une share the same katakana (レディアン), though Une has a dot between the ィ and the ア.
Shinji of Neon Genesis Evangelion and Judai of Yu-Gi-Oh! GX both have two love interests named Rei and Asuka, with the same but reversed color schemes (white and red) to their wardrobes.
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.
There are two characters with the name Saten. One is from Railgun who is one of the protagonists and the other one is from Needless who is an antagonist. Please don't mix them up. Oh wait, do it. You'll get a laugh out of it.
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 Coola'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.
Speaking of Yomi, there's also Ayumu "Osaka" Kasuga from the former series, and Kekkaishi gives us an interesting name combo of a character called Yomi Kasuga.
The Robot Girl character from Mahou Sensei Negima! and the bar where Akemi works as a waitress in Maison Ikkoku both have the same name: Chachamaru. The spaceship from Plastic Little also has this name, except that it's usually punctuated as "Cha-Cha Maru".
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.
K-On! has an aspiring musician-cum-moeblob call Yui who plays guitar. Angel Beats! also has an aspiring musician-cum-moeblob call Yui who plays guitar.
The British dub of Space Carrier Blue Noah referred to Hidaka as "Alan Carter", which is the name of a character from the British science fiction series Space: 1999.
Crossing over with Real Life, a drama CD was released starring five different male characters all voiced by seiyuus whose first name is Daisuke.
Intentionally invoked with Kimi ni Todoke. Whether you're referring to the anime/manga, it's first season OP, it's second season ED, or it's live action version's theme, they all mean the same thing.
The main hero in both DragonBall and Saiyuki is Son Goku, a Sajin with a staff. It's because both stories are based upon Journey to the West, whose main character is named "Sun Wukong"*
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 that 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.
