Mark occurrences is not a new feature, but the trunk contains some improvements in this area. In the source the feature highlights in the elements which is under the cursor position. You can also easily move between marked occurrences through ALT + UP and ALT + DOWN shortcuts.
I'm going to show you some differences. On the pictures there is on the left side screenshot of NetBeans 6.5 and on the right side screenshot of the same source, but from NetBeans 7.0 development build.
Class fields are also marked in the PHP doc.
Parameters of a function or a method are also marked in the PHP doc.
Types are marked in the PHP doc as well.
NetBeans are now able to mark the same methods in method chains.