As long as there is no simple to use software managing bibliographies for (this feature should be added in the next 3.0 version), LATEX is still the only way to write scientific papers, containing tables, figures, numbered equations and references, for free. However these applications are only dynamically linked to Microsoft Word.
Of course, expensive software like Endnote of Reference Manager can do it. For all of us who had one day to write a report or even better a thesis, managing the references is always more or less a nightmare.