When I started to read the book 'Zend Studio for Eclipse Developer's Guide' by Peter MacIntyre and Ian Morse, I was particularly interested in those types of [features you haven't discovered yet]. And luckily it contained many of these.
Ivo mentions one in particular that he found interesting, the "Working Sets" that lets you define a set of files within a project that you want to work on. There are a few places where it falls a bit flat, though. He didn't like the code examples that included PHP4 in some places and that the book started off with preferences for features you hadn't even been introduced to yet.
Considering however the overall usefulness of the book in learning the details of the Zend Studio environment, I'm willing to look beyond those weak points, and recommend the book to those that develop in Zend Studio for Eclipse on a regular basis.