Even as awesome as Final Fantasy X's intro FMV and Final Fantasy XII's Vayne transformation (which I had to leave and go tug on myself after that one)... I still have to go with Final Fantasy IX's Alexandria FMV. That game has some of the best FMVs... and that one probably wins it all.
XD Horny bugger.
I have to go for Bahamut VS Alexander. I can watch it over and over again. Pivotal point in the game too.