One example of such a law could be a death penalty law. In fact, in Furman v. Georgiain 1972, the Supreme Court ruled that death penalty laws could be constitutional per se but could be unconstitutional as applied to individual cases.
In that case, Justice Stewart held that the death penalty itself was constitutional, but that it was being applied unconstitutionally. This was, he said, because the law was not being applied in any sort of a consistent way. Instead, he said the laws were applied in ways that made them seem capricious and arbitrary.
So, a law giving the death penalty for specific conduct might be constitutional per se, but be unconstitutional as applied if it is not applied consistently to all defendants.
Religous beliefs and expression is constitutional per se. However, if that belief excites hatred and murder of others in different religions, then it would be unconstitutional.
Another example is freedom of religion, which is constitutional per se. Nonetheless, for a teacher in a public school to teach or force his/her religion onto students would be unconstitutional. It could also violate separation of church and state laws.