That's a bit vague and broad. Name one conflict that was fought under the premise of doing the wrong thing.
I phrased it badly. In these cases, both alliances pretended to be protecting human rights, international law (by breaking it) etc.
You state both as fact, people are still arguing over the WMD's still not found, being moved, projects that sought to aquire them. Same goes for genocide, or other generally unpleasant things that went on in Kosovo.
Well, people will always argue, but I care only about the facts. No serious WMD threat was found in Iraq, and no signs of genocide were found in Kosovo.
What if someone was to think that one was an evil regime, while the other wasn't? That in one case there was a case for going to war, while in the other case there wasn't.
Such a people would be the biggest hypocrites in the world. Saddam was clearly one ofthe most brutal and oppressive dictators in the world, responsible not only for 2 senseless wars, but also for brutal oppression of all three major ethno-religious groups in Iraq.
Miloševič was a liberal democrat, compared to Saddam.
From any serious POV, Saddam's regime was worse that Miloševič's, and it commited much worse atrocities.
Regarding Iraq/Saddam, many say it's good he's gone, but the reasons for going to war were crap.
So were the reasons to go to war against Serbia in 1999.
Again, just because someone believes a good case was made for one invasion, that doesn't mean he has to support every other invasion. Even if they has simularities, which many invasions have.
If such a person wants to protect his moral integrity, he has at least explain why is the other case different. Many people of this type I know were against the 2003 Iraq war only because they don't like the Americans.
They are always conducted by the good guys, accoording to the invading party, against an evil regime, accoording to the invading party. If that's your case for simularities, the Germans were led to believe the Poles were babykilling savages because of Josef Gobbel's CNN. They believed they were in their right to get Danzig back in the reich and save the Germans from the muirdering and raping Poles.
WW2 was a totally different story. Germans never pretended to be protecting some international system based on law, they left the League of Nations, therefore their actions happened outside this framework. Also you omitted the fact that Nazi Germany was a totalitarian dictatorship. You can't really say that about NATO countries, unless you're some kind of Communist nutjob, which I know you aren't
NATO in Yugoslavia argued that it acted on the premise of self-defence (the only situation when a country is allowed to independently use power according to the UN Charter) of its interests

It said that a military action was necessary to stop something, what now appears to be a huge hoax.
Coalition in Iraq argued that Saddam's WMD's and support for the terrorists make him one of the most dangerous dictators in the world, and that his opposition to the UN inspections justifies military action.
As I said, the only difference is that Serbia was demonised by most of Western media. Journalists simply used the bad reputation Serbia had after wars in Croatia and Bosnia and in their lust for another such war, they grossly exagerrated the real situation in Kosovo. This influenced the public opinion, afraid of another Bosnia, and indirectly the politicians, who had to act on the basis of completely wrong infromation. The secret services did a great job as usual (their "success" was later repeated during 9/11 and then in the time preceding the second Iraq war), so the NATO started a war which was not necessary and as Storealex said, it was waged in a wrong way.