This of course is totally subjective, and everyone who has visited or lived in Japan will have their own favorites, but I can tell you what I know after living two years in Nagasaki-ken:
There are many seasons for specific noodle dishes in Japan and noodle specialties vary from region to region and even city to city. Come in the summer months and you will be delighted by cold noodle dishes like mori-somen and mori-soba, come in the winter months and you can eat the tastiest udon or soba as well. My personal favorite noodle dish which is served year round in Nagasaki-ken is Champon. It is of Chinese origin and combines veggies and seafood in a pork based broth.
Also of note anywhere in Japan is the ramen. Not to be missed, especially after a night of sake drinking!
Ittadakimasu! almost 8 years ago
Well, here are some great resources:
A blog that reviews 345 Ramen places in Tokyo:
And here is a Noodle database web site (although it's all in Japanese so you might need Google translate!) http://ramendb.supleks.jp/
My personal favourite from my last trip in April was a place on the island of Shikoku - but alas I can't remember the name. almost 8 years ago