Excluding the ones already listed (most of which I would have listed), my top favorite Wolf's Rain AMVs are as follows:
Description: As you may be able to infer from the title, this is a character profile about Darcia. It's a two-part AMV which shows the character's downward spiral from nostalgia to insanity.
Description: Though it doesn't have any particular point or storyline like 1, this AMV is simply delightful to watch, as it has great action sync and uses footage that most AMVs don't. I also like the music choice.
Description: a very emotional AMV that seems to capture the tradgedy in Wolf's Rain well, even though I wouldn't really call it a sad AMV
Description: It actually took me a few times to like this one, then, well, I just fell in love with it.