Yuuki Cross/Kuran VS Rido Kuran a.k.a. her uncle. One of the best battle scenes in shoujo, ever. Especially because the shoujo herioine is so badass. Also: "Stop saying my name!!!", "I am not my mother!", and Rido caressing Yuki before he dies. This is especially awesome because Yuuki herself killed him.
Chairman Cross kicked major ass in chapter 45.
Speaking of Cross, the scene close to the end in chapter 41 has become one of his most absolutley famous scenes, where he hints at just how badass he can be and proves it in the chapter 45 scene mentioned above.
Juri Kuran sealing all her daughter's vampire instincts and turning her into a human to save her life.
Also: The chapter 45 flashback where she talks to the currently-vampire hunter Kaien Cross. Just... read it.