The haunted house at Fuji-Q Highland in Yamanashi Prefecture is supposed to be one of the biggest in the world. According to the
website (English version available), it takes a whopping 50 minutes to go through.
I went to Tokyo Disneyland last year on Halloween day, and it was pretty fun - though so crowded that I only got to do a handful of attractions. Lots of Japanese people were dressed up in costumes, especially in themed groups. I remember one group that was all dressed up in some expensive-looking Alice in Wonderland playing card soldier costumes, and another group of about 15 people dressed as dalmatians (for 101 Dalmatians, of course).