I think one of main amv that I saw on beginning of my No.6 journey were Utopia and shattered, Utopia, beautiful amv mostly topic around whole story of no.6 with both characters and city:
First Nezushi amv I saw, quality wasn't great but I still love this song, it fit perfect to those two, and how creator put quotes from anime into it.
From one of my favs now, and I have many of them on my playlist:
Hurt:
Start slowly but turning out amazing in the end. I love part "All I know goes away in the end" amazing fit Nezumi
Fallin away:
Simply love it.
Not alone:
Beautiful and one of better mixed amv with both anime and manga.
For now last but there are more amazing amvs around YT
lover dearest