I used to be a big fan of Netbeans (i think i still am), but now i'm using PHPStorm, and is really great... the feature that is really helpful to me is the Refactoring; that works like a charm in Codeigniter projects, i refactor a lot my code, all the time, optimizing here and there and the tools that have PHPStorm makes this a lot easier and safer.
just my two cents =:-)