Off the beaten track in Tokyo

Will be going to Tokyo in a month for the second time this year.
It'd be great to get some ideas about places to visit which are a bit out of the ordinary.
I'm into design, games, movies, art and Japanese pop culture. I'd love to explore everything from hidden, traditional restaurants to Alcatraz ER (been there).
Explore areas which are not mentioned in the tourist books and their local shops and restaurants. I'm going to Shimokitazawa. And I'll return to Daikanyama (didn't really find too much there the last time; where are the cool shops?).
Any suggestions?

Nobody have really been any special places or found some hidden gems in Tokyo?

Yes but if we give addresses everybody and their dog will go there!. Hint: look at the Yamanote loop line map and check all the neigbourhoods you have never heard about in any of the guidebooks.

Yeah if we put them on a message board on the web, they wouldn't be so secret or hidden anymore would they. I also did what the previous post said, just get on a train line you've never been on and just get off wherever you feel like. You'll probably hit more duds than not but I'm sure you'll uncover some gems too.

I liked the trip with the Toden Arakawa line as it brings you through parts of Tokyo where hardly a tourist comes and I enjoyed to see where Tokyo-ites live.

http://hoshisato.aminus3.com/image/2008-08-23.html

Suggestion: Buy a museum pass, also known as a grutt or grutto pass. Although it isn't a secret, it will motivate you to get into some different parts of Tokyo.
http://www.museum.or.jp/grutto/about-e.html

There is also a good package deal that isn't mentioned on the English site: for an extra 800 yen over the cost of the pass you can get two all-day tickets for the Metro. (If you're interested in this deal, buy the pass at the commuter pass booth of a Metro station.)

I bought a pass for the first time in May of this year, and it took me to many places in Tokyo that I have never been to before. I had a ball with it.

it's kind of pointless to ask about off-beaten places to go on a message board meant basically for tourists in japan.

if you're going to be in tokyo, just try taking a couple local trains and getting off at random stops, especially stops with not many people around. you'll need to speak japanese in these kinds of places though, no one will be able to speak english.

take a walk a few minutes from stations and check out the shops and restaurants.

it's not going to be THAT interesting, if it were, lots of gaijin would already go there. sorry!

Well. I think you misunderstood. All I am asking is if any of you have been places you've really enjoyed. That be an area, a small restaurant or a hidden shop (as mentioned I'm into art, japanese pop culture and stuff).
For example... a nice street in Daikanyama, a cool book shop you came over, a particular bar in Golden Gai... You know what I mean?
Just some ideas.

Come on people, the Lonely Planet forum's Japan section has some great suggestions for this kind of thing, surely we can make some! Mandarake might be worth checking out, it is several floors of different shops that is considered manga, anima and cosplay geek heaven and is an insight into an aspect of modern Japanese culture- if you really want to you can shell out for a vintage anime figurine- some of them go for several thousand dollars!

Mandarake is in Nanako, at the end of the Nakano Broadway arcade. Nakano is one station from Shinjuku on the Chuo Line (orange line).

Also check out this site- I think you'll find a lot of good stuff here:
http://www.quirkyjapan.or.tv/

And here is a really off-beat website, check out the Tokyo information, some of the buildings he talks about are truly bizarre (have seen pictures).
http://www.hellodamage.com/tdr/travelguide.htm

Thanks a lot. That's more what I was looking for.
I've already been to Mandarake in Shibuya. Great shop.