To narrow the FMV's down to a definite best out of all the FF's is an impossibilty for me, so I'll try to pick out the best for each individual FF intead.

FFVII- Plenty of great ones here. There's Aeris's Death, Sephiroth's "In the Flames" scene, the "Emerging of the WEAPONS", That one WEAPON getting his head blown apart.... I gotta go with the FMV when the WEAPONS first came from Earth. The sense of actual fear I got from that was just classic.

FFVIII- You can say whatever you want about this ff, but it is undeniable that some of the best FMV's in video game history came from FFVIII. The elegance of the Ball Room scene, the real choreography of the parade scene, the sense of calamity when Galbadia attacks Balamb, all unforgettable. But the best would have to be that Intro scene. Oh...My... GOD!!!

FFIX- Don't remember many FMV's from this one. The scenes where the Eidolons were being summoned (namely Atmos) were awesome. But the ending scene get's the award here. I remember my little sister crying when she saw it!

FFX- The FMV's from this ff escape me a bit as well... For now, I'll just say the long first scene where Sin attacked Tidus's original world....