Organization LIX/YMMV

Hilarious in Hindsight: In "Thrill A Minute" released in December of 2008, Axel is referred by to his (then unknown) real name of "Lea," pronounced just as it would be in the Japanese version of 358/2 Days released months later.
Tear Jerker: The ending of "Namine's Day Out".
Viewer Gender Confusion: Vexen's voice actor, Ryuu, gets this a lot.

Funny Aneurysm Moment: An exasperated Sephiroth muttering about Zack and Angeal: "I swear, someday they'll both going to get themselves killed". Yuffie rants to Zack about how she will become a sexy, fishnet wearing ninja with tons of adoring fans, to which Zack exclaims in amusement: "Sure, and I won't live to see 25."