Square Enix didn't present a ton of news at this year's Tokyo Game Show, but here is a summary of their announcements:

The 3rd Birthday:

Aya Breya will be shooting... things in Japan come December 22, 2010.

Kingdom Hearts: Birth by Sleep Final Mix:

This release, which will likely be exclusive to Japan, adds the extras from the North American version of KH:BBS, plus a few more additions such as an unlockable "secret episode".

Dissidia Duodecim

Tifa has been confirmed as the final playable character from FFVII. The game will be out in Japan next spring, and the Japanese version includes some cross-promotional costumes from other Square Enix games: Lightning has an Aya Breya costume and Cloud can turn into his Kingdom Hearts form.

Here are some screens distributed to the press at TGS:

Fabula Nova Crystalis Games:

There were some short trailers of Final Fantasy Agito XIII and Final Fantasy Versus XIII shown at the conference, but the segment was blacked out to the public. Square Enix announced that they will hold a conference for Fabula Nova Crystalis (the name under which the compilation of all three FFXIII games is known) on January 11, 2011. Famitsu reports there is unlikely to be any news about either game until that date.