What really makes an AMV for me is timing (if everything hits the music just right I'll really get into it), suspension (there has to be some kind of an idea going on behind the AMV, some kind of a plot no matter how confusing, and in Bob's name no repetitions or looping the same scene more than once!) and how well the AMV fits the general mood of the original series.
Here's the one that prompted this whole entry. Sayonara Zetsubou Sensei AMV done with killer style. There may be a little pun in the previous sentence wink wonk. Seriously put this AMV captures the spirit of the original flawlessly and I'm watching it now for who knows how manyeth time because wow!
Ok, Princess Tutu; this is not a new one to probably anyone but I believe it really does earn its place as one of the all-time best AMVs ever made. Simply beautiful.
...ok I could not leave this one out. It's simply too hilarious, and if you know this scene from D. Gray-Man you'll know it's quite a stark contrast to what actually happens in the scene that most of the AMV is made out of, and there's absolutely nothing funny going on there. If anything for me this was the first moment of D. Gray-Man when I realized I was in for a ruthless and somewhat traumatizing a story (but of course I love Tyki Mikk - I mean who doesn't?).
Lastly, my own favourite. There hasn't ever been and still is not a single AMV that would top this one for me. It's got everything I look for in an AMV, also holy wow the maker really found all the coolest moments of the medicine seller! Besides there's a bit of a joke included in the selection of the song - it's "Let's Go! Onmyouji!"