There is the Square Enix cafe with many Tokyo locations to choose from, one in Osaka, and now one in Shanghai! Then there is Artnia and the Eorzea Cafe, which are a focused on the high end art and goods, and the mmo, respectively.
Update: added some photos of last visit to the Akiba cafe at Akiba station, the entrance is tiny but has some nice and probably exclusive stock!
The Square Enix Cafes
?101-0028 Tokyo, ????Kanda Hanaokacho, ??1,
(aka First Floor Yodobashi Camera Store Complex, Akiba)
Also branches in Osaka and Shanghai
The Akiba cafe seems permanent but please check websites before visiting, some may be pop up locations (only temporary).
The catering is run by Pasela, the same company who run the Capcom cafe and quite a few others. The cafe goods area is reportedly small and food… not so good.
As a shopper you can just walk straight in, and don’t forget to check the 2nd floor upstairs! Don’t expect old items to be in stock, so it may be better to dig around Akiba.
There are also stores in Osaka and Shanghai.
The cafe will have different themes per season.
Eorzea Cafe
1 Chome-1-10 Sotokanda, Chiyoda-ku, T?ky?-to 101-0021, (Akiba)
Just through the bridge enclosing Akiba. It has better reviews for food, even though the company is the same – probably because it’s less busy. It is of course more aimed at the JRPG side. May not have a wide selection of items on sale.
Artnia
?160-0022 ????????6?27?30 (Shinjuku Station)
Has a bigger range of (and far more expensive) items and is next to the actual Square Enix offices. Food has better reviews. Cannot guarantee Sephiroth will be here, you need to go to the gallery part of the store. Just walk in, and over him.
For good FF themed food, book in advance and maybe you can beat the 2 hour wait…
There are other stores at Harajuku etc that may or may not be permanent, check the website for locations and current themes.
Storia
A new store with emphasis on music and game events. Also features collaboration themes such as Seven Deadly Sins, better check before you visit!
Storia Site (Ikebukuro) | Storia Map