Shirou Kamiya

Break the Cutie: Seeing several of his friends/classmates breaks him as a person, including when Joan of Arc succumbs to the same fate as her clone mother.
The Everyman: He's the point-of-view character whose initially seen as the token "not clone" of the series, until the reveal that he too is a clone, just not of a historical figure.
Fish out of Water: As the seemingly regular student of the academy, he's lost to everyone else's pasts and the clone parents they live up to.
Ordinary High-School Student: Shirou is the only non-clone at his school. Until it's revealed he is in fact also a clone.
Scholarship Student: Shirou fills this role in a lot of ways: he's allowed to attend the school only because his father is headmaster, he's a bit of an outcast among the students, and he provides an everyman for readers to identify with. However, obviously, this isn't because of money but because he's not a clone. Or so he thinks.
Stranger in a Strange School: Shirou's the only non-clone in a school for clones. Or not. He is, in fact, a clone of the school's founder.

Elizabeth Tudor

Cheerful Child: This becomes disturbing once Hitler starts losing his sanity.
Face–Heel Turn: He leaves with Elizabeth and Kai at the end of volume 6.
The Atoner: Hitler feels guilty for the things the original Hitler did.
You Cloned Hitler!: He's a Hitler clone struggling with the dark legacy of his genetic father.

Driven to Suicide: [[spoiler%He can't take the pressure of living up to his original. Luckily, his attempt to hang himself fails.]]
Hates Being Touched: At least by non-clones so this mostly applies to Shirou since Shirou is usually the only non-clone around.
Insufferable Genius: Although his belief in his own genius turns out to be the source of the insecurity that drives him to suicide.
No Sense of Personal Space: Once he figures out Shirou might be a clone, he constantly invades the other's personal space to taunt him.

Faculty

Abusive Parents: Dr. X was... Not a good father.
Stranger in a Strange School: Like Shirou, he was the only non-clone at a school for clones. Unlike Shirou, he was the real deal.

Other

Killed Off for Real: During an attempt to run for student council president, he gets shot in the middle of his speech.
We Hardly Knew Ye: He only appears for several panels before being shot, kicking off the subplot of clones worrying they'll succumb to the same fate of their clone parents.