Chiang Kai-shek's Kuomintang government in China (the ally people always seem to forget) committed one of the worst (and least talked about) war crimes of the entire war.
In 1938, as the Japanese army was advancing south toward Henan's provincial capital of Zhengzhou, Chiang desperately needed time to bolster the city's defenses and halt the Japanese. He did this by destroying the dikes along China's Yellow River. The river overflowed and huge portions of the Central China Plain were flooded, effectively stopping the Japanese movements for months.
People always talk about the Nanjing Massacres in the context of the Second Sino-Japanese War, but we hear very little of Chiang's decision to flood the Yellow River. Yet the death total was catastrophic. The initial flood, and its resulting famines and disease, killed somewhere between 500,000 to 800,000 people. The Nanjing massacre resulted in the deaths of (this is the highest count) of 300,000.
It's true that the nature of the Nanjing war crimes may be considered more horrific by some (and indeed the accounts are heart breaking), but Chiang's decision to destroy the dikes was a crime against his own people. That gives it an especially black legacy. Perhaps some will rationalize that the Japanese invasion put Chiang and his government in an impossible situation in which they were forced to make terrible decisions to save the state. Chiang's diary does reveal remorse for the decision. Regardless, as war crimes go, it may have been the single most destructive event in the entire war.
See, Rana Mitter, Forgotten Ally: China's World War II. 2013
Yes and No. The answer depends on who wins the war.
Lets look at a few examples shall we!
I am going to take the nukes off the table because that's too easy (Not saying it was a crime, just a lot of people call it out.)
Bombing of Dresden specifically and in general Allied air raids on cities that killed hundreds of thousands. Look to Tokyo, Berlin, Dresden, Hamburg and several other cities. We prosecuted people in Nuremberg for these crimes when they where committed on us.
Rape. The rape of Germany. Holy crap, The Big Red Rape Soviet Machine laid waste to the German civilian population. Estimates go up to the millions with ages as young single digits. Don't think the US was completely clean either, post occupation Tokyo had rapes in the hundreds, but it was no where near the scale.
Unrestricted submarine warfare was carried out by the US and Germany yet we prosecuted Germans at Nuremberg for it.
POWs. Hundreds of thousands of German POW's and civilians died a HARD death in Soviet prisons during the war and after. Also the US in the pacific had a nasty habit of mutilating dead Japanese soldiers for trophy's and photos.
Troop ships. Soviet subs sunk several evacuating troop ships with civilians as well as wounded aboard. Some of these ships had up to almost ten thousand people aboard. Wilhelm Gustloff had nine thousand aboard killed, Goya and Armenia had 7k each lost. Junyo Maru was a Japanese ship that the British sunk with over five thousand dutch POW's on it, all dead.
These are the obvious stuff that would be prosecuted. But by far not the only ones.
War Crimes are really grey area in that only the victor really gets to point the fingers. In reality both sides in any war will do some real rough stuff. But the loser can't complain in general.
Here some wiki links.
http://en.wikipedia.org/wiki/United_States_war_crimes#World_War_II
http://en.wikipedia.org/wiki/Soviet_war_crimes
Be warned the soviet section will take a while to read.