The main difference between the join and the apply operator is that the apply operator can be used to "join" the result from a function.

If you use the apply-operator using a subselect it might be the same than using the join-operator.

In my experience the apply-operator is more likely to use the subselect as a sort of loop and executes the subselect for each outer row. But also this: not always.

If you expierence differences in your performance you have to look at the execution plans.

If you are not familiar with reading execution plans save them and post them here (save it as am XML, NOT as a screenshot.

You can also try to create an example and post it here so we can have a detailled look at it.