The most memorable meal I had in Japan was in this little restaurant, Kyushu Jangara. It was the best ramen I have ever had in my entire life and I grew up going to the Japanese enclaves in Los Angeles! Kyushu Jangara specializes in Kyushu ramen, which was made famous by Hakata (now Fukuoka) in Japan. It's full of flavor and the noodles are perfect consistency. My mouth waters as I describe it. Make sure you stop by when you are in Harajuku!
If you ever had Japanese ramen, it will blow your mind. I go there everytime I'm in Japan. During lunch time you definitely have to stand in line outside. Akihabara store is very small but tastes better than other locations.
Favorite Dish: Bonshan has a very thick soup base and comes with cod roe and slices of pork. So delicious that you'll ask for a second.
Everytime I've been to this place I've always seen it packed with Japanese and not so much gaijins (foreigners) -- a pretty good indication that the restaurant is legitimate with the locals. It's a small restaurant perfect for a quick bite to eat.
Favorite Dish: Try the Jangara or Honshan ramen. Lots of goodies in there that makes the ramen MmMm MmMm gooooood!