Love Hina (anime/manga (better)): two people promise to go to Toukyou university together, but the girl moves away, and the boy does not remember her face or name. However, later, despite failing to get in a few times, he continues to try out for the same school, and he meets a girl who also wants to go there for a different reason.
Ef - a Tale of Memories. (anime): the girl has always liked the boy, but he has no clue. When he meets another girl, his childhhood friend starts making her move.
Ef - a Tale of Melodies. (anime): boy and girl used to be at an orphanage, but the girl left. Years later, they reunite in high school.
Ef - a Fairy Tale of the Two. (manga): the girl has always liked the boy, but he has no clue. When he meets another girl, his childhhood friend starts making her move.
Ayu Mayu (manga): the boy gets separated from his little sister at an orphanage when she is adopted. Later, he seeks her out, but it turns out she could one of two girls. He fights his feelings for them, because one of them could be his sister. Also, another girl from the orphanage appears as well, having liked the boy since he used to help her.
Akikan! (anime/manga): girl likes boy, boy (though a pervert) is clueless (at least for a while).
Ichigo 100% (anime/manga (better)): four heroines, one is a najimi (childhood friend) and hints are shown.
Hanbun no Tsuki ga Noboru Sora (anime): not much happens between the boy and the girl, but it is there.
High School of the Dead (anime/manga): well, it does fit the requirements. The girl promises the boy she would marry him when they grow up, but he does notice her feelings until she dates his best friend.
School Days (anime): they met in middle school, and used to hang out a lot, but they went to different classes in high school. After a while, as he is dating someone else, the girl decides to go after the boy.
True Tears (anime): she likes him, he thinks of her as an older (though shorter) sister.
Pastel (manga): she makes her move at the wrong time.
Onegai Teacher (anime): they go to the same high school, but he secretly marries the teacher, who is an alien.
Girls Bravo (anime/manga): she bullies him, and he has an allergy towards girls.
Yomeiro Choice (manga): she has a crush on him, but cannot admit it even to herself. He has to worry about his future children. (Read it to understand; very funny.)
B Gata H Kei (anime): she is shy and likes him, but he likes the school idol (or "queen," as she calls herself (wait until she meets her rival)).
I"s (manga): she is energetic and likes him, but he likes the school idol.
A Girls (manga): they both like each other, but have yet to confess.
IO (manga): she says he killed her mother, he has no idea whom she is.
Fortune Arterial: Akai Yakusoku (anime): they used to play together as children, now he barely remembers her. She (along with others) seems to like him, though.
Myself; Yourself (anime): they used to be among a group of friends, but he left. When he comes back, she acts cold towards him, but still displays jealousy when he talks to another girl.
Hatsukoi Limited. (anime/manga): aside from the siblings, one of the boys likes his older neighbor, being a part of a love triangle.
Tonagura! (anime): they were neighbors, but he moved. Now he is moving back, her hopes are up, but . . .
No Bra (manga): they were at an orphanage, but got separated. Years later, one moves in with the other in high school, and something shocking is revealed. [Not Recommended]
Sandglass of Summer Colors (OAV): the boy likes the school idol and wants to confess to her as summer break is starting tomorrow. He encounters a suspicious person, and is surprised to wake up at the beginning of the new semester. Everyone consoles him, and he discovers that they were dating during the elapsed time, and that she died the day before. His childhood friend hugs him as she cries and says it is her fault.
Clannad (manga): she acts tough in front of him, but her real feelings start surfacing.
That turned out to be longer than I thought it would.
