There's a rumour that Eiko is the name of Sakaguchi's daughter or wife and Aki is the name of Sakaguchi's mother as in the credits for ff:tsw there are 2 ppl, eiko and aki sakaguchi
The beginning of the battle theme of FF9 is actually identical to the beginning found in FF4-6. Uematsu dropped this beginning for all FFs afterwards bar 9.
The music in Gulgu volcano in FF9 is another reference to FF1 as FF1 had the same dungeon with the same music.
Lord Avon and the play is a reference to Shakespeare and Romeo and Juliet. Shakespeare was born in Stratford-upon-Avon and the play uses old elizabethan language and the two lovers that should never be together and the tragic ending.
Beatrix is actually a character very similar to that of Leo in Final Fantasy 6. Both characters were good hearted generals that worked for the wrong side. Both characters were very powerful and have Shock as an ability. Both characters realise the wrongs of their ways and eventually side with the heroes.
Items won at the Auction house are also references to early FF's. Une's Mirror (Une is a character from FF3), Rat's tail (as said earlier by someone, a key item needed to upgrade classes in FF1), Matoya's Potion (Matoya is a character from FF1).
Taking certain key items to the Black mage's village will allow you to unlock a music track that was first heard in Final Fantasy 3.
