My exposure to the country outside of brief stops in Osaka, Kyoto, and Yokohama has largely been in Tokyo. Sort of like basing an opinion of the U.S. on visiting Pittsburgh, Tacoma and New York City. Since my opinions are virtually flawless if not laughable, I'm hopeful you'll allow me some latitude.
In retrospect, I've consumed some seriously odd food and drink while visiting Japan. As a tourist and visiting company colleague the quantity of random food that my incredibly hospitable hosts have put in front of me is staggering. There is a reason though: I'll eat and drink any weird shit these men and women are willing to put down their own gullets.
I've eaten various forms of "nankatsu" also known as soft bone. This is usually a meat item with some sort of bone still involved which you're expected to eat. Is it juvenile to admit I blushed when when of my more attractive female hosts asked..."Scott San do you like the soft bone?" The chicken nankatsu is sometimes found in yakitori restaurants and is pretty gag-inducing if you don't know what you're in for. I actually ate some sort of chicken sashimi once too. Better have an alcohol-based beverage handy...
Speaking of which, Japanese beer is a good accompaniment and dry and innocuous enough but the real libation worth checking out is Shocho, a clear distilled spirit in theory vodka-like. The primary difference between sake and shochu is that sake is brewed while shochu is distilled. Shochu is distilled from various ingredients which have some form of fermentable sugar to be converted to alcohol before the distillation process. Typical shochus are made from potato, rice, wheat, and barley. Without getting too technical, there are two types of shochu: Otsurui (single distilled leaving good flavor of source ingredient and served straight) and Korui (distilled multiple times and usually used in cocktails).
This beverage is fantastic and isn't quite as strong as gin or vodka and has amazing flavor and usually comes served with one or two giant, carved, pure ice cubes. Shochu came in handy last week when I ate one of the more odd items I've consumed at a sushi-oriented restaurant. No it wasn't some uni-infused item, highly overrated fugu or saba liver sashimi rather it was ika no oduri gui...live or dancing squid from the Izu Peninsula, 60 miles south of Tokyo.
The squid was brought to the table still alive with part of its flesh cut up and placed on it back. It was still breathing at this point, its tail and eyes still actively moving. I have to admit as your loyal glutton, this was weird as hell and for a fleeting moment I felt bad. After we ate the delicious top layer the plate was removed and the balance of the sea creature came back later delicately fried with panko. Fantastic! The night ended in Rappongi district with the requisite karaoke which is always a highlight.