One of the most memorable eating out experiences we ever had in Tokyo was Uoshin in Nogizaka. We were sitting on crates, drinking highballs, nihonshu, and beer and the sashimi and fish dishes were fantastic. Prices were reasonable, atmosphere was really great. Coming back to Tokyo soon, and we'll definately be back.
Can anybody recommend other places like this (cheapish izakaya, great atomosphere, nomihodo set, not too far to travel from shinjuku station).