In terms of quality and graphical impressiveness, the two easy winners from this generation are any and all FMV's from Ninja Gaiden, and most major FMV's from FF X-2. Both just scream capability, whether you like them or not.
Onimusha 3's intro. rocked, so that has to be considered as well, but my favorites will always be in FF VIII (intro., some in between, and ending). Not sure why.