Netbeans has a plugin for doing UML. Using this you can create analysis diagrams that include your classes (therefore their methods and attributes). If your pages are also classes, then you don't need more.
But basically you won't find something that allows you to also structure both your codes and pages all together, it doesn't make sense to me, you have to create your own diagrams in these cases (see Dia: http://projects.gnome.org/dia/)
Edit
Gotta check if the Netbeans UML plugin does convert to PHP output. It sure does for Java, but haven't tried for PHP.
I've just come across http://argouml.tigris.org/
It has PHP support and seems really nice. I also found: http://www.gentleware.com/