As mentioned, the first Arc in Naruto. THE BEST ARC IN NARUTO:
When The loss of Haku hits Zabuza and through Naruto's speech, he realises Haku is... gone. After killing Gatou, he asks Kakashi for one last favour before he dies, which is to take him and lay him besides Haku.
In Fullmetal Alchemist... Greed's Death. Even Ed cried when he realised what he done, and that Greed weren't such a bad person
The Ending for Grave Of The Fireflies actaully, **** it, the whole film made me feel like a bitch when the, umm, "Setsuo" died (Is that her name? Hmm.). Brought a tear to my eye... easily one of Studio Ghibli's best.
And last, but not least, Wolf's Rain Tsume's/Hige's/Toboe's and Blue's Death with Hige's + Blue's being the most dramatica. Where they layed besides each other knowing that they were going to die and asking Kiba to "put them down" (Kill them).