Sorry that this is late... just saw this today.
In Shimokitazawa I went to a concert at Club 251. Just before then my friend Paranda recommended I try this particular shop known for Gyoza... and get the crab & egg dish.
http://www.ohsho.co.jp/
http://www.ohsho.co.jp/menu/east/rice.html - top middle dish.
The gyoza came out within 30 seconds of ordering them and I had just seen the John Oliver sketch about Chinese food arriving a little TOO fast so I was laughing internally.
Good stuff, highly recommended.
In Asakusa (where I normally stay) I went to this Chinese place for XLB... ripoff... spent like nearly 5000yen and didn't enjoy the food much.
http://www.asakusaimahan.co.jp/english is close to my hotel and looks impressive... didn't actually go inside.
http://nabe-zo.com/lan_en/restaurant_search_en/ is great for Shabu Shabu (AYCE with Ice Cream and Japanese Curry on the salad bar-ish area)
http://www.wako-group.co.jp/en/ is my favorite chain restaurant for Tonkatsu (those baby clams in the miso soup, I usually get two bowls...)
Japanese music producer I'm FB friends with recommended this -
http://www.geocities.jp/poem_feel/nodaiwa/ (160 year old restaurant??)
also...