I'm based in Japan and have to fly in and out every few months for work. Here are my observations:
1. It used to be pretty relaxed. It still is... if I'm traveling with my wife. For the last 18 months, every time I've flown by myself, I've had my bags briefly searched and been given a pat-down by customs after re-entry. (It may be because I wear a kilt.) However, when they do search my bags for whatever reason (hasn't happened in departures for at least 4 years), they apologize and repack everything nicely for me. This is unlike my experience in American airports where my bags are rifled through, and then I'm expected to repack it-- and get yelled at when I can't undo their unpacking job within 15 seconds.
2. Actually, with the fingerprinting, visa-holders get to use their very own line, separate from even the Japanese citizens (since citizens don't get fingerprinted... just us dirty, criminal (and in my case, permanently residing, tax-paying, etc.) foreigners). I'm usually through faster than anyone else, since there are so few of us on any given flight. But even so, passport control is FAST. Almost as fast as the EU: I've experienced fast passport control (i.e. pretty much a walk-through) in Copenhagen, Helsinki, and Paris. The fingerprinting and face photographing sucks and makes me mad. But it is really quick.
3. Outbound security is relatively strict, but also quick. A breeze compared to the U.S., Canada, the U.K., or, ugh, Charles de Gaulle (they confiscate soft cheeses in carry-on now, but you're never informed of this when you check your luggage for the flight that connects you to France). That's right, France, I'm going to blow up your plane with my Camembert!
4. I much prefer flying into and out of Narita than I do flying in or out of any international airport in North American, France, or the U.K.
Mommy, what happens to your files when you die?