Having finally now gotten caught up with 3.2 storyline and the new Hildibrand quests.... there are a few more interesting references to past FF games that have slipped in that have not yet been mentioned (spoilered where necessary)
FFIII
In the Antitower dungeon, mammet enemies are fought, one of which is listed by it's attire and nameplate as a 'Viking' - 'Viking' is a Job in FFIII.
FFVII
A quite obscure one, especially given the battle's obvious FFVI origins and connections, but, a subtle nod to name similarities with the real name of FFVI's Fiend in the Sephirot battle to FFVII is made with the achievement for the completing the Sephirot EX trial - 'Veni Veni Vendias', is a reference to a line in the last stanza of the lyrics of One Winged Angel, which, of course any FF fan worth their gil should know is Sephiroth's seminal final battle theme in FFVII - thus alluding to the similar names. 
FFIX
During the second new Hildibrand quests,
a mammet attired in traditional BLM attire (yellow witch's hat, blue robe, green and white striped pants) named 'Gigi' is discovered - the name and his appearance are clearly based on Vivi Oriniter from FFIX (even more so given Vivi's artificial nature in FFIX).
The newest Veteran Reward for ongoing subscriptions is the 'Tantalus attire' - this is actually the costume of Zidane Tribal, the main protagonist of FFIX (the name 'Tantalus' references the name of the theatre troupe/band of thieves that Zidane was a part of)
FFXI
The design for the 'Gloria airship' mount that is an achievement reward for winning 200 battles in the new PvP event 'The Feast' seems to actually be based on the design of the Jeuno airships (albeit shrunk down considerably) from FFXI
FF Tactics
During the new Hildibrand quests features a bumbling zealous Ishgardian Inquisitor named Cyr - he actually seems to be a combination of two very different characters from FFT:
his appearance of blue robe and long blonde hair tied back in a pony tail clearly is meant to reference Ramza Beouvle, FFT's main protagonist, while his personality and status as an inquisitor is more similar to characters like Algus.
There's probably more, but this is what I've uncovered so far.