To set up SubEthaEdit to open .class and .inc files in PHP mode you will have to edit the following Info.plist file which is inside the SubEthaEdit application bundle:
SubEthaEdit.app/Contents/Resources/Modes/PHP-HTML.mode/Contents/Info.plist
with PropertyListEditor.
You will find an array called TCMModeExtensions where you just have to add the elements inc and class.
Hope this helps!