Israel/Palestine

For example, a murderer in New York is sentenced in the same courts under the same laws, regardless whether that person happens to be an American or an illegal immigrant. In the occupied territories, there are two different legal systems, one is completely unfair and the other is a normal justice system of a democratic country. That's a clear example of Apartheid when one group is legally discriminated against and have no civil rights.

If the Palestinians in the occupied territories were part of the same legal system like they would be in every other democratic country in the world, that particular part of the Apartheid analogy wouldn't stick. If the Palestinians had equal rights, or even separate but equal rights there would be no basis whatsoever for the Apartheid analogy.

There are of course other reasons for the Apartheid analogy, like the fact that State land in the West Bank and East Jerusalem is for Jewish use only (!) and that Palestinians can't legally access natural resources, including water, which literally prevents all forms of economic growth. The Palestinians aren't allowed to expand existing communities or build new ones, while Israel is building new settlements all the time. There are no circumstances where Israelis and Palestinians have equal rights.

Here's a report from Human Rights Watch about Israel's treatment of Palestinians that doesn't mention the A word:

Separate and Unequal: Israel’s Discriminatory Treatment of Palestinians in the Occupied Palestinian Territories
Source: Human Rights Watch, December 19, 2010