From tomorrow people going to Japan will have their fingerprints scanned and then they will be photographed. There are more info on Japan Probe  and on the brand new blog Re-entry Japan.
This new immigration procedure is pretty annoying but the good side is that foreign business man and (non otaku) tourists will think double before going to Japan. Of course gaijin otaku travelling offr their pilgrimage to Akihabara will not bothered at all as the procedure resembles something from sci-fi mangas and anime...  so if you are taking an airplane to Narita today choose a good T-shirt (no Greenpeace nor human/animal rights defence T-shirts). The safest choice is anything from Cospa even tought complete  costumes could create some problems (I'm curious if they will allow kigurumi or Danny's Star Wars Stormtrooper suit for the photos).
Of course this new immigration system is a joke since foreign yakuzas (that control the Pachinko businees) are already living in Japan and other criminals usually are illegal immigrants that will be even safer since the police will not have their fingerprints nor their photos. Terrorist have always been Japanese since in centuries no gaijin has  committed an act of terrorism in Japan (beside the Yamanote Hallowen Party ^_^)!
Anyway better being scanned than having your DNA registered like in Europe (France and other countries are working on this idea)...