I don't think it's necessary anymore, but I'll put this up in case it will help anyone else traveling to Japan.
People who want more detailed advice should make it clear how long they plan on staying and what their budget is.
秋葉原 (Akihabara)
If you want to visit manga, anime, game, cosplay, figurine, and maid shops, you ought to spend at least one week just in Akihabara.
I recommend the store "Mandarake." You should go to as many stores as time allows, though.
http://www.youtube.com/watch?v=G_yMkBttqo0
http://www.youtube.com/watch?v=Ha5lzDm9evc
http://www.youtube.com/watch?v=xMUfRw1W_74
http://www.mandarake.co.jp/shop/index_cmp.html
池袋 (Ikebukuro)
乙女ロード (Otome Road) is aimed at (female) yaoi fans.
Pretty much the only other things I can think of are ジュンク堂書店 (Junkudo Bookstore) and サンシャイン60 (Sunshine 60).
http://www.youtube.com/watch?v=r74i5Wy9vbw
http://www.youtube.com/watch?v=WEvCAq3dxjU
http://www.youtube.com/watch?v=6X4SJvv5KoA
渋谷 (Shibuya)
You can see the street fashion on 渋谷センター街 (Shibuya Center-Gai), but its value to otaku is questionable.
There
is an otaku-oriented Shibuya Mandarake store.
http://www.youtube.com/watch?v=QXtOdSgf6Ic
http://www.youtube.com/watch?v=eC1ThHxHocA
http://www.mandarake.co.jp/shop/index_sby.html
原宿 (Harajuku)
You can see Harajuku's street fashion on sunny weekends.
You can also go to Yoyogi Park.
http://www.youtube.com/watch?v=ATXxuEqr5p8
皇居 (the Imperial Palace)
http://www.youtube.com/watch?v=f_KUIhm8Pwg
浅草 (Asakusa)
http://www.youtube.com/watch?v=taBxjvtpCAg
江戸東京博物館 (Edo Tokyo Museum)
http://www.youtube.com/watch?v=57nHrOqL36w
Don't go to 築地 (Tsukiji)!
The tuna markets are popular with foreign tourists, but are often closed off to said foreigners, as the market officials are hindered by people with bad manners.
All in all, it seems like they can do nothing but drive out all the visitors.
http://www.youtube.com/watch?v=8N7biyHCY0Y
http://www.youtube.com/watch?v=tzBwtylHiqo
http://www.youtube.com/watch?v=flkGDrAeDqs
山谷 (Sanya)
There are cheap inns here. It's close to Akihabara. You're fine if you can speak English. The rooms are small!
http://www.youtube.com/watch?v=-8_VXlWCNhU
http://www.youtube.com/watch?v=IbBGeaUfXfM
http://www.youtube.com/watch?v=kNWt4nx3Vk8
http://www.newkoyo.jp/index.html
大阪 (Osaka)
Osaka is the birthplace of Ayumu Kasuga. It's the second largest city in Japan. It's the center of comics. The food here is delicious.
オタロード (Ota Road) is located in 大阪日本橋 (Nipponbashi, Osaka).
http://www.youtube.com/watch?v=69A3aL3Yrs0
http://www.youtube.com/watch?v=Ud2M_iMifFo
http://www.youtube.com/watch?v=AdZpBaGH9zc
http://www.chuogroup.jp/kita/index2.htm
京都 (Kyoto)
There are lots of temples and shrines here. Some famous ones are 清水寺 (Kiyomizu-dera), 金閣寺 (Kinkaku-ji), and 銀閣寺 (Ginkaku-ji).
http://www.youtube.com/watch?v=u5njZhbhL9s
奈良 (Nara)
Pretty much the only things I can think of here are deer and large Buddha statues.
http://www.youtube.com/watch?v=BV3d3qUUk7o
http://www.youtube.com/watch?v=ZIb8f53230E
ブックオフ (Book off)
It's a chain store for used books. They're all over Japan.
http://www.youtube.com/watch?v=RzFRgkTL2wQ
サンリオピューロランド (Sanrio Puroland)
http://www.youtube.com/watch?v=9-s2LryyC0Q
http://www.puroland.co.jp/english/welcome.html
ポケモンセンタートーキョウ (Pokemon Center Tokyo)
http://www.japan-guide.com/forum/que...y.html?0+37042
http://www.youtube.com/watch?v=0ThqWRht6lE
三鷹ジブリの森美術館 (GHIBLI museum, Mitaka)
http://www.ghibli-museum.jp/
新幹線 (Shinkansen, Japanese bullet train)
http://www.youtube.com/watch?v=mn5wjOvZiVo
Comiket
It's a festival that's held twice a year.
Comic Market 78 will take place at 東京ビッグサイト (the Tokyo Big Sight) from Friday August 13th 'til Sunday the 15th.
http://www.youtube.com/watch?v=5AtKqEZ8Kdk
http://www.youtube.com/watch?v=dNdQMoRxfeg
漫画喫茶 (Internet cafes where you can read manga)
They have between approximately 15,000 and 60,000 manga books. Usually, a shop will have around 20,000.
The division between smoking and non-smoking sections are often poorly managed, and may be tough for non-smokers to handle.
It can be cheaper than an inn to stay here if you use the bundle fees to your advantage.
http://www.youtube.com/watch?v=ScOfA_y_Hmc
http://www.youtube.com/watch?v=vPaXNG-dbzU
聖地巡礼 (Pop-culture tourism)
A pastime where people visit places from anime and manga and such.
I wouldn't recommend it for people who aren't staying long.
http://www.youtube.com/watch?v=1bzaR3HZ0Qc
http://www.youtube.com/watch?v=0g5mTllPpvE
http://www.youtube.com/watch?v=NeRFhE2Rj1U
http://www.youtube.com/watch?v=xfmDm_MKGv0
日本のトイレ (Japanese toilets -- Washlet)
These are commonplace in Japan.
http://www.youtube.com/watch?v=gJazvumHNyk
http://www.youtube.com/watch?v=HM4nP7khZ5k
スーパーマーケット (Japanese Supermarket)
I'd like you to think this is the only store that carries "MyNuts."
http://www.youtube.com/watch?v=QYHzyLrtvBY
100円ショップ (100 Yen Shop, Dollar Store)
http://www.youtube.com/watch?v=ZEb0b1GEaE8
コンビニ (convenience store)
They're generally 24-hour stores. You can buy candy and bento boxes, and stand around reading manga and magazines among other things.
http://www.youtube.com/watch?v=0J2ZTdMRfRM
容器 (containers)
http://www.youtube.com/watch?v=KlwoCWIeYtU
弁当(Bento)
These are common in Japan.
http://www.youtube.com/watch?v=0qkSh5ylLDQ
明治きのこの山(Meiji-Kinoko-Chocolate-Mushroom-Cookies)
Try eating some.
http://www.amazon.com/Meiji-Kinoko-C...dp/B000W4OQRW/
メロンパン (Melon Bread)
Is it true you don't have this outside Japan?
http://www.youtube.com/watch?v=vTXZqPHDfmk
http://www.youtube.com/watch?v=BHrfjbQujto
吉野家 (Yoshinoya)
http://www.youtube.com/watch?v=39MILG4txBk
キューピーマヨネーズ (Kewpie Mayonnaise)
http://www.amazon.com/Uwajimaya-Kewp...dp/B00023T3IA/
日本のストレートパーマ (Japanese Straight perms)
http://www.japan-guide.com/forum/que...y.html?0+16576
What Not To Do In Tokyo: The Top Five Tourist Mistakes
http://www.jaunted.com/story/2010/3/...urist+Mistakes