Another reference off the top of my head is during the ending, when (SPOILER)

Tantalus is performing "I Want to be Your Canary", one of the character Marcus' (played by the thought-to-be-dead Zidane) lines was "No cloud, no squall shall hinder us!".

Which was a tribute to the main characters of the previous two PS1 Final Fantasys (and sort of clever because it makes sense, if you consider that a squall is a sort of small storm).