In Japan, it was Douglas MacArthur's skill at re-ordering the government, the media, and the social structure that kept insurgencies at bay. He didn't want to purge the Diet or the industrial machine of every possible militarist collaborator; he knew that a complete sweep would result in a failed state. So he executed the worst of the worst and put the rest of them on notice.

It didn't work perfectly well. MacArthur was at constant odds with some Japanese officials and industrialists. He handled it with a classic American "my way or the highway" approach. If one of these men acted like a thorn in MacArthur's reforms, he would hammer that man down. He used a graduating set of responses: rebuke, public humiliation, re-assignment, prison, or even the gallows. MacArthur needed these men, but he didn't need all of them.

There was also a significant communist movement that threatened the new occupational order. As you can imagine, MacArthur didn't like it. But he knew he couldn't go about imprisoning or executing every political dissident. Instead, he used the media. Under MacArthur, newspapers, magazines, radio, and film flourished like never before. The Japanese realized a new level of self-expression. And they liked it.

But there were rules. One could not publish or distribute anything that was critical of the occupation, glorified militarism, or that supported communism. These rules were non-negotiable. By robbing the communists of any hope of gaining larger appeal from the masses, their effort fizzled out.

MacArthur's occupation was effective because it was largely peaceful and it gave the masses some hope for the future. A nation that expected to be burned alive after capitulation was instead brushed off, stood up, and given food, medicine, and a somewhat free press. (There were hundreds of newspapers and magazines dedicated solely to helping families re-connect in the aftermath. They were immensely popular and everyone knew they had MacArthur's stamp of approval. Things like this helped the Japanese people ease into acceptance of the occupation and "endure the unendurable".)

Source: "Embracing Defeat", John Dower

EDIT: typo fixed.

Ill elaborate a bit on how the Western Allies handled the situation. It is important to realize that, near the end of the war, Germans had pretty much lost all faith in the war. They realized that it was over. Hitler did too. That is why he was hellbent on detroying Germany itself, figuring that if the Germans could not win the clash of civilizations, they were better off being eradicated. So Hitler himself wasn't all that popular anymore either.

Another important element is the fact that the allies learned from the first world war. Completely sanctioning Germany into oblivion was pretty much one of the main reasons World War 2 happened, so that was a no-go area. Most of the German population was therefore spared from harsh sanctions. German POW's served in forced labour for a few years after the war, mostly working to clear areas of undetonated bombs and mines, but that was put to a stop after people started pointing out that this was essentially slave labour. The most severe sanctions were laid upon high-ranking Nazi officials; predominantly people who joined the NSDAP before 1933. For the most severe offenders, death was deemed the only suitable sanction.

So you can imagine that, for most Germans, the defeat was something of a relief. It was finally over. Of course, not everyone was happy about it, and I'm not saying that conflict between Germans and the western Allies didn't occur, but I've not heard of any major altercations between Germans and the western Allies.

Sources:
Maarten van Rossem - De Tweede Wereldoorlog in 28215 Woorden
Sebastian Haffner - Anmerkungun zu Hitler

What about fascist Italy? How where they treated after the war

Lots of comments in this thread giving huge weight to the effect of the US-occupation in Japan. Not so much from the Japanese point of view. Would love to hear more about that.