You might want to give "BEIGE" a try -- it is the new Alain Ducasse restaurant on the top floor of the new Chanel Building in the Ginza in Tokyo. Apparently, the food is served in a series of small portions (complaints of being too small have been made) with very light or minimal additional seasoning/dressing to let the natural flavours of the product shine through. It just opened this month and they should have any wrinkles in the kitchen/service ironed out by the time you get there.

There is also a thread I started about Atelier de Joel Robuchon Tokyo in this forum in which several FTers have commented on and suggested other great french restaurants in Tokyo. Notably, there is a Cafe Troisgros, a Taillevent Robuchon, and a Caves Taillevent in Tokyo. Nobu Tokyo seems to be fairly popular for lunch. Il Teatro, in the Four Seasons Chinzan-So, is considered to be among the best Italian restaurants in the city. Ekki in the Four Seasons Marunouchi is also supposed to be excellent.

There is also a thread on having sushi for breakfast at the Tsukiji Fish market which you may want to look at also.

For a quick snack, check out the food floors, typically in the basement floors, of Department stores. Each "stand" has samples of their wares, go around to several them "sampling" the food and you can make an interesting snack out of it!!!

I will be trying a couple restaurants when I am in Tokyo in January (haven't decided yet) but will also report back afterwards.