A couple suggestions;
Atsuta Shrine - Houses the Kusanagi, and is considered one of the most important shrines in Japan. (But as it isn`t in Tokyo or Kyoto, it doesn`t get too many foreign tourists.)
Ise Shrine also, if you haven`t been there. Also one of the most important shrines (the most important from a religious standpoint...)
There are some smaller, out of the way shrines that I find absolutely wonderful... but they`re smaller and a bit out of the way.