Comment Rational Rose, Enterprise Architect and StarUML (Score 1, Interesting) 200
Enterprise Architect is very nice, since you can do forward and reverse software engineering with it.
However, if you do not have the budget allocated for it, a good compromise is StarUML,
which became very nice and usable lately and has the same "feeling" and menu-driven approach
like the old Rational Rose and Enterprise Architect:
http://staruml.sourceforge.net/
http://sourceforge.net/projects/staruml/files/staruml/5.0/staruml-5.0-with-cm.exe/download
As for Rational Rose, the first original version was very good with some known quirks until it
became IBM Rational Rose and was converted into a "super Eclipse" plug-in.
So, if you enjoyed drawing UML diagrams in the old Rational Rose,
then Enterprise Architect and StarUML are the tools that you are looking for.
And if you do not like to draw with a mouse then Graphviz Dot and a good text editor is for you:
http://www.graphviz.org/Download.php
For tracking issues / documents and schedule,
I can recommend either BugZilla, Mantis or BaseCamp:
http://www.bugzilla.org/download/
As for the actual writing part, your company should already have a good set of Word Templates,
to document the actual Sofware Requirement and Specification (SRS), Sofware Design Document (SDD),
Change Request Document (CRD).
Once, you got those set up, then we mostly use MantisBT or BaseCamp to share, comment and track them.
As for producing code documentation, the choice are: Doxygen, JavaDoc, NDoc, JsDoc:
http://www.oracle.com/technetwork/java/javase/documentation/index-jsp-135444.html