Eric Posner deals with the question of whether it's fair that Saddam should be put on trial but not Bush. He goes through the litany of charges that are thrown at Bush, and shows that it's difficult to pin on him war criminal status. But his major focus is not whether Bush is a war criminal, but whether it would make sense for states to try him as one. And to this question he answers no, because many of Bush's wrongs were policies of previous American administrations, not to mention leaders of other (even democratic) countries. Furthermore, trying Saddam can accomplish other worthwhile political goals.
Such is the fate of international criminal law. Because much of the law is based on custom (notwithstanding the ICC), and there's little agreement as to whether a norm has been sufficiently followed to fall into that category, there can be little prosecution in the international realm on international criminal grounds. It's difficult to justify prosecution of war criminals for a violation of international law unless one admits that the trials are just political and are not based on any form of international law.
However, Saddam's trial is in Iraq and is being prosecuted by the people of that country. So we avoid the problem of having the victor punish the loser. If Bush is a war criminal and the US would be trying Saddam, perhaps the claims of unfairness would have some teeth (although Saddam would be a fair greater criminal). But the people he harmed are trying him. The grounds on which he is being tried are the breaches of international human rights, but Saddam never allowed the people to exercise their will by outlawing the methods of murder he utilized. Perhaps as a strictly legal matter, his trial violates due process (if we assume international criminal and human rights law do not really serve any purpose), but as a political and moral matter the people of Iraq trying Saddam is completely just.