Off the beaten track for Tokyo?

My next trip to Japan will be my 5th time visiting this beautiful country.

I'll be only in Tokyo (and only for a few days), and since I've already visited all the touristy spots, I am interested in seeing other lesser-known parts of Tokyo.

Have you guys got any suggestions in the way of cool spots to photograph, places to eat and neat things to see that aren't necessarily in guide books? "Off the beaten track", as it were?

Thanks :-)

Nokogiriyama

How much of Tokyo have you explored previously? Yanaka? Shimokitazawa? Daikanyama? Todoroki Valley?

About 95% of Tokyo is away from the touristy spots. Do you want to confine yourself in the 23 wards, one of the 39 cities in Tokyo prefecture, or would you consider the greater metro area including Kanagawa, Chiba, and Saitama. Plus there are heaps of day trips you can do that most tourists never do (Fukushima Aquamarine is pretty good).
I recently had a request for "rural" Tokyo and looked into Oku-tama and Hinohara which are close by.
One interesting resource is Tokyo in 91 days http://tokyo.for91days.com/

Best way to do that is to just pick train/subway station you haven't been to, get off the train and start walking.

Which gardens have you seen? What time of year are you going?

Suggestion: Take the Chuo Line "Azusa" Express from Shinjuku, Tokyo, (or take the Highway Bus if you're on a budget) to the end of the line, Matsumoto, and from there go north by local train about 20 or 30 minutes toward Omachi or Hakuba and get off at any stop. For starters, the view of the Japan Alps will blow you away. Walk, borrow a bicycle, whatever. You'll have a great time, see some awesome sights including many traditional buildings, and enjoy some interesting foods.