There's some really good spots near Waseda University. I ate at a spot back in June but totally forgot the name. There's also an AMAZING spot in Chiba city, owned by some friends of friends.

From my Japanese friends:

1) Menya Musashi Bukotsugaiden in Shibuya. (pics/loc http://worldc.am/id/4b55b1dcf964a52026ec27e3)

2) Ippudo, which is a chain, in Shibuya, Takadanobaba, or Kichijoji. (pics/loc http://worldc.am/id/514af015e4b007e18e9b53ac)

3) Nakamoto in Shibuya. Spicy ramen. (http://worldc.am/id/4b601ccef964a52031d629e3)

4) Orenosora in Ikebukuro and Takadanobaba. (Pics and location here: http://worldc.am/id/4b5be0dff964a520451b29e3)

5) Butoka in Nakano and Waseda. (http://worldc.am/id/4b7a7afdf964a520202e2fe3)