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don't forget to check out the museum in the Mori building (Roppongi Hills) if you like modern art! Plus you can pay a couple hundred yen extra for admission into the observatory for some awesome views of the city (it's on the 53rd floor IIRC)
there's also a parasite museum in Meguro, although it's kinda hard to find since it's not a major tourist attraction.
If you're thinking of getting off the beaten path, I highly, highly recommend that you buy the Tokyo City Atlas. It puts google maps to shame, and is a must-have for anyone that wants to do some serious exploring of Tokyo on foot. Since the address system in Japan is so chaotic (in comparison to the American standard), having this book really saved me a lot of time and frustration in figuring out where I needed to go. Of course, if you have a functional smartphone over there, then I guess it's not really necessary, but it still might be handy to have a physical backup