For example let's say I have an app that uses $_SESSION['user_id']. Now if I have two of these applications running on the same server then they will be sharing this user_id variable which would break things.
The only thing I can think of is to prepend some unique id like this:
$_SESSION['/application1/user_id']
$_SESSION['/application2/user_id']
This is the purpose of session_name(). Assign a different name to each application's session to avoid collisions between $_SESSION keys. The name will be used as the session cookie's name so although both session cookies will be passed to both applications, only the one matching the application's session_name() will be used to populate $_SESSION.