Another reference I remember is in that enchanted forest when Zidane has to collect the fragments of a story and piece them together, that story he collects is the plot of Final Fantasy 2.
When I replayed FF9 on PSN to review for the site, I renamed Garnet/Dagger to "Keris" because it's a really cool looking dagger: http://en.wikipedia.org/wiki/Kris
Black Mage Village is one of my all time favorite town themes.
Several of Mooncalf's parody fics for FF9 are amusing (http://mooncalf.org/library/parody/) but my favorite is definitely Eiko's Boyfriend: http://mooncalf.org/library/parody/eikosboyfriend.html (Tell me that's not how the final battle should have ended!)
This one is funny too: http://mooncalf.org/library/parody/wwtomato.html
My favorite part is still in Lindblum when Zidane comments on a cheesy suit or armor in a shop, then later on Steiner goes into the shop and comments on what a fine suit of armor it is.
I liked it, can't you tell? http://www.rpgfan.com/reviews/finalfantasy9-psn/index.html