In a new post to his site Stoimen Popov makes the recommendation to not call the destructor explicitly in your code and provides some alternatives.

PHP 5 introduces a destructor concept similar to that of other object-oriented languages, such as C++” says the documentation for destructors. [...] Well, as you can not call the constructor explicitly [...] so we should not call the destructor explicitly. The problem is that I’ve seen this many times, but it’s a pity that this won’t destroy the object and it is still a valid PHP code.

He talks about __destruct and it's role in PHP's set of "magic methods" and what they exist to do. He then gets into a few examples of what code could look like that uses a destructor and the difference between normal handling calling the destructor explicitly. The main differences is that calling it explicitly does not destroy the object, it's basically like calling any other method. He does include an interesting method for destroying the object - setting it to null - and notes that the destructor fires then too. He also points out a few interesting things about cloning objects and how object references work when setting nulls as in the previous example.