So, I have finally scanned through this thread and I have to say that I've found only three AMVs that caught my attention.
MySpaceTV Videos: Naruto and Sasuke's Final Conflict by hehehe...>83 - this one originally posted by sasuke91 is a good one. Although I don't like Naruto (or rather I'm scared of its monstrous amount of episodes), I do like Naruto AMVs.
YouTube - Jihaku. Foo Fighters-Best of You - AMV posted by Powermad147 is really well made and interesting, too.
YouTube - 【MAD】 Death Note 『Spoil』 - thank you Kiyuge for this one. My personal winner from this whole thread. I loved Death note, and although I'm not so fond of this type of music I must admit that it's goes perfectly with the atmosphere of death note. Also the visual effects are just amazing.