Updating my list.
#4 RahXephon-Frou Frou-Euphoria *No Serious Spoilers*
Won so many contests I lost count, and it deserves every one of them. Nuff said, watch the vid!!!
http://www.youtube.com/watch?v=P38ZVmYNkmg
#5 Eureka Seven-Spoken-September *SPOILERS!!!*
When I said a good AMV could make you like a song you hate, this is what I had in mind. Spoken is a Christian scremo band, which is a paticular type of music I avoid at all costs. This however is a great example of good song choice. The lyrics are very similar to the plot of the series, and so it works. This one is really just for fun, nothing that fancy or original but I like it anyway.
YouTube - We Are Not Alone