For a real hole in the wall experience in Tokyo, have yakatori under the tracks. There are a bunch of these little joints under the JR circle rail line, in roughly the area between the Imperial Hotel and Ginza. They're very popular with salarymen after work, sort of like very modest happy hour bars, but if you like grilled chicken and beer, this can be a light dinner between evenings spent in top restaurants.

Another idea for a very modest meal that could be considered to be comfort food is to go to a place specializing in noodles.

For foodies, it's always fun to go down to the basement food hall of a top Japanese department store to stroll around and look at the variety of local products sold by different stalls, including the very fancy fruit and melon (a hundred dollars a piece, with a nice bow tied around the stem in a velvet lined wooden box) that's intended for gifts.