[ZephyrLeanne]

I'm from Chubu, really [Shima, Mie], so I don't think I can really be very biased here

But ANYWAYS. I don't really agree with spending a WHOLE week in Tokyo. 2-3 days should max it. I think you can do this: Buy a Japan Rail Pass, fly in from Kansai Airport and leave via Narita. I say so because the queue immigration for arrival in Narita for foreigners is very long, more so than Kansai. But it's not where you want to be flying back from, since duty-free is [almost] non-existent and airport tax is super-high.

Originally Posted by Shii

Places you will sadly miss: Saihou-ji, Byoudou-in, Kouzan-ji, most of the cafes. It's OK, I missed these things too.

Fine to miss, really. Not worth the time.

Places you can feel free to miss: Imperial Palace, Ginkakuji, Kinkakuji, Ninnaji, Hieizan, Daikakuji, Nijojo, Heian Jingu, Ujigami Jinja Shimogamo Jinja, Nishi and "Higashi" Hongwanji. These places are for scrubs. (Note: I'm betting if any Kyoto residents read this they will hate me)
Places to loathe: Kyoto Tower[/QUOTE]

AH. Agree with all EXCEPT that I feel that you can drop Kyoto ALTOGETHER.
I'd agree with Shii for the Tokyo part... but let's go thru the recommendations, yes?

[QUOTE]

You'll want to dedicate about a lot of time to Akihabara. If you've only got a week you should wake up early, get on the train, and spend the day walking around. The best places there are undoubtedly Toranoana and Don Quixote, and basically everything else you can find yourself if you really look closely. See if you can find the 2ch goods stores. This is obvious, but ignore the English speaking cafes and stores because they are aimed towards clueless "Fujiyama, geisha, Zen" foreigners. ...

^^ The truth. You'd want to try the first/second train. Really, because the trains get packed very easily after 7. The worst is on the Yamanote line. [It's famous for a reason]

Ignore Ikebukuro unless if you are an otomen.

NO!Although it's aimed at otome, it's not too bad, really. And since it's about 200m only, it's not too long and can be easily fitted into plan. Just avoid the after-work hour[s].

In fact, I think the two [Akiba/Ikebukuro] can take a whole day

Most of the doujinshi fairs are in Tokyo. Fairs occur on almost every weekend in Japan and if you only go to Comiket you are missing out on real doujinshi culture. Go to http://ketto.com/ a week before you leave and find out what's good. They generally cost $10 or so to enter, and even if you don't buy anything you may be treated to cosplay, copibon, and other such fun stuff. Most of these are NOT in Akiba so plan ahead. This is also a fun chance to get to be a foreigner who stands out, because on the streets of Tokyo or in a cafe you are generally considered an irritating tourist who can't speak the language, but if you go to a doujin fair some people can be all like

If you are up for a local trip the Ghibli Museum is the most obvious thing to do. You need to reserve tickets about a month in advance. In order to get in you will have to find a Lawson near your hostel and ask the cute Japanese girl at the counter how to buy museum tickets. Don't get nervous! If you're not going to be in Japan for a month you have to buy tickets through JTB.

This, you've gotta do your homework, I can't help you here.

If you actually have the time to enjoy Japan on non-otaku merits-- and if you're anything like me you will get tired of Tokyo culture within 24 hours

Make that 48. You'd want to buy a PASMO in Tokyo, in addition to a JR Pass.

-- you should take a ride to Kyoto, which has like a dozen World Heritage sites, and Nara, where you can act out that scene from Lucky Star.

Sorry, I disagree. Besides, Lucky Star scene was in Saitama.
And, I think you should go to Osaka and Kobe next, if for the food. Real Japanese food is to be had in Osaka, not Tokyo. Tokyo's food is like business-class, Osaka is first-class Japanese food [along with Hakata].

In Osaka, you'll want to spend a half-day in Nipponbashi, the Akiba of Kansai. As well as Shinsaibashi [but start as Nagahoribashi station, where Crysta Nagahori mall is]. Both are on Sakaisuji Line on Osaka's subway.

In Kobe, be sure to visit Disaster Reduction Museum, but it may be a little out of the way... Well, the architecture of that plot where the DRM stands is quite striking as well.

I seriously think that Nara isn't worth your time, but the Kyoto guide above may or may be suitable, depending on what you're looking for.

AFTER Kansai, then you should go to Tokyo. Which is why I say: arrive at Kansai, depart at Narita.

Cheers.