There were a lot of huge problems in more recent years with the loop line thing. Way too many people showed up, and they were blocking commuters from getting on the train... Unless they were cute girls. Someone we know was literally pushed from the train.
It really got ridiculous, from what I understand. It is one thing to have a small and fun tradition, but it is another to start kicking normal people off the train, stripping down, breaking things, and just generally creating havoc. It had reached the total havoc point with those riding having an attitude of "you can't touch me, screw anyone not participating"...

The backlash came after a couple years of serious problems caused by the riders. If the ride has disappeared, good riddance in my opinion. There is no need to make reasons for discrimination. *sigh*

ETA;
Back on the original topic...
I will second what Cola said. Most haunted houses and "scary" type attractions disappear with the end of the hot weather. It is seen as a way to have a chill in the hottest months of the year, and is also linked to Obon (festival of the dead) which is in mid-summer. Autumn is not the time for ghosts in Japan.

A ton of things to do
 

Halloween is a big weekend for me every year. On the Saturday closest to Halloween (29th this year), Roppongi is rich with costumed bar-hoppers after 10pm. Many of the foreigners wear thoughtfully crafted costumes whereas Japanese drinkers, who have realized that most people are in costumes, crowd the Don Quixote store buying the last of the novelty costumes. Many bars offer a gift or free drink to those who wear elaborate costumes.
On the Sunday closest to Halloween (30th this year), Kawasaki has a huge Halloween parade. It is bigger than events I've seen in the states and the attendees are very serious about their costumes. The homepage is here: ラ チッタデッラ【川崎】～KAWASAKI Halloween 2011
If you want to be in the parade or enter the contest, you have to register on the website. Register early as they reach capacity quite early in October. Here is a video that I recorded at last year's parade (I am the guy in Iron Maiden's Eddie costume at the beginning and throughout the video): Japanese Halloween Parade - YouTube
Metropolis has a Halloween Glitterball on a weekday before Halloween weekend (This year on Thursday 27th), but who can really get out on a weekday? Somehow it's still a very crowded event. This is the online ticket sales: Metropolis Glitterball 2011 - The Monster Bash
Finally, there is a regular ghost tour in Tokyo. They usually do a cemetery walk on the Saturday night closest to Halloween. It is a good tour, but it is full of creepy facts or murderous stories rather than walking into a possibly haunted house. In other words, it's more of an interesting dark history tour. It has great reviews. Haunted Tokyo Tours
The attached photo was taken at an early evening hour in Roppongi. It gives you an idea of the crowd. I am Michael in this photo.