Sushi Dai at Tsukiji Market is one of the best meals I've ever had in life. If you don't want to line up, I'm sure Daiwa Sushi next door is just as good although I think you get more for your $37 (approx) at Sushi Dai as well.
Eat at the convenience stores. Not even kidding. When you come back, you will WISH our 7-11s were like that. I once had a spaghetti carbonara from a Family Mart that was
fucking delicious. Seriously.
SkinnyPupp and I really like Torigen. I believe there are a few of these in a few different areas of Tokyo.
Cold soba and udon from just about any ol' place will be delicious on a hot summer day. I actually sort of prefer udon. For truly masterful soba, check out Kanda Yabu Soba.
Here's a few more along with a bunch of other stuff I wrote about Tokyo when I lived there for a summer four years ago:
Japan 2008