It's not that she tries to keep to herself, exactly: It's just that everyone seems to look right through her! Naturally, Sakuya Tohno has a complex about it. She says she's just like air: ever present, but never seen. All she wants is a friend, but building relationships isn't exactly easy for someone who is, for all intents and purposes, invisible. But then she hears a legend about the "Thousand-Year Sakura" and how, if one makes a wish beneath its perpetually-blossoming boughs, it's sure to come true. So in a moment of desperation, she races to the tree, only to find four very attractive boys waiting for her... And at that moment, beneath the cherry blossoms of the ever-blooming Thousand-Year Sakura, something incredible happens!
(Source: Turtle Paradise)

Shuichi comes back after a long absence from school to find his old friend Kura. No one else remembers Kura though. After searching Shuichi ends up at an old western style house where he finds Kura in the basement, in a coffin!?

From Nevermore Scans:
"From now on, I will destroy you..." This bewitching, heartrending, most wicked boyfriend appeared in front of Kana!? A dangerous and sweet new serialisation starts!
Takachiho Kana who attends a distinguished private school is bright, well-behaved and extremely soft-hearted no matter what the time. She's neat, and doesn't seem to have any problems, but she carries a darkness within her heart. On the night of the full moon, the world around her starts to grow loud.
The meeting that changes Kana's fate is already drawing close.

[From PresenceDear]:

After his pet rabbit dies, Hiro becomes friends with a classmate who resembles his former pet.

Astarte and Touwa are two girls who act as "Undertakers," people who deliver the final messages of the departed to their loved ones.
In addition to trying her best at her job, Touwa is also attempting to deal with her growing feelings for Astarte, and there's also the question of their shared past...
(Source: Horobi no Michi)

On the eve of her sixteenth birthday, Kozue Hiyoki is visited in her dreams by a man who steals her heart- literally! Determined to find him and retrieve her stolen heart, Hiyoki, with the color of the man’s hair and the tattoo on his chest as her only leads, enrolls in the S-Hall dormitories of St. Nazareth Academy, but quickly realizes that its residents are not at all like she expected… For starters, they’re all guys!

There, Hiyoki soon discovers that she has the ability to look inside her dorm-mates’ dreams, which may be the key to uncovering the identity of the thief who stole her heart…. But perhaps her biggest challenge is that most of the guys won’t let Hiyoki into their rooms, much less their hearts!

Most girls are crazy about jewelry, but not Anis Yamamoto(Barajou no Kiss). Not since her father gave her a rose choker as a child, claiming it was a protective amulet which would safeguard her from harm; however, if she ever took it off (a feat easier said than done!), she would be afflicted by a “punishment” of some sort.
Not like it matters to her though, since the attention it attracts around school from faculty and students alike isn’t something she’s particularly fond of.
But after a certain incident causes the choker to disappear, she realizes that this punishment her father spoke of might have been a bit more than she bargained for!
Although the female leader(Barajou no Kiss) starts off as an outcast because of her ghostly appearance, she gradually begins to make genuine friends by simply being herself and her kindness.
And she falls in love with the most popular guy in school who is genuinely nice, reciprocates her feelings, and is the first person who sees her for who she really is, though she's too socially awkward to realize this at first.