What to visit in Tokyo/Kyoto?

[TheCracker]

I'm going to Tokyo/Kyoto for 3 weeks at the end of January, and I'm a manga/anime and videogame Otaku, so I would like to know what I should visit there.
Thank you

[Dagger]

I lived in Kyoto for a year, and I've been to Tokyo several times, so I can give you a lot of suggestions... but I guess it depends on what you're interested in. Do you like Japanese food? (Beyond standard fare like sushi and tempura, I mean.) Are you interested in historic/cultural/scenic destinations, or just stuff related to modern pop culture? How much time do you plan to spend in each city? Feel free to throw questions at me/us, too. The more I know about your preferences, the easier it'll be to help you out.

All that aside, though, you're going to have an absolutely amazing time. Both Tokyo and Kyoto are too awesome for words, and there's just so much to do.

[TheCracker]

Actually I've already been there some years ago so I have seen most historical and cutural stuff, like the temples. What I'm looking for is more like "secret" things you should visit as an otaku.

[CaNz]

but those are a secret! I can't tell you about them

[Dagger]

Well... I dunno what qualifies as "secret," but perhaps the most purely otaku thing you could do would be to attend Comic City Tokyo, which will take place on January 23. (Comic City Osaka is on January 9, but it sounds like that's before your arrival.) It's a Comiket-esque (located at the same venue and all that) doujin convention.

Going by memory, there isn't any major corporate participation like at Comiket, but there's a really cool area where people sell a huge variety of original artwork in various forms--postcards, prints, folders, stationary, etc.--as well as handmade goods and accessories. I would almost say it's worth attending for that and the overall experience alone, even if you're not that into doujinshi.

I'm at a loss for what to recommend in Kyoto; I mean, I guess you could stalk Kyoto Animation and Nintendo? ^^;; If you have a favorite anime or manga or game that takes place in/around Tokyo or Kyoto, it would be fun to go visit the real-life versions of places featured in it (which is what I did in Venice for Aria, haha). Of course, that might not be applicable to any of your favorites.

[TheCracker]

I don't know if I will be in Tokyo at the right time for Comic City, but thank you