Most effective free software for publication-grade structure diagrams I have done extensive research on trying to find free software that I can use to create publication quality structure diagrams with but have yet to find something suitable.

Tools I currently know about are:


Xmind
Freeplane
FreeMind


And then there are a bunch listed here.

The problem with all of these are that they either make mind-maps that have quirky stiles that don't look very technical/professional or they don't support PDF or PS or high quality bitmap exporting.

I really like XMind, but the free version export totally rubish quality bitmaps and no PDF.

I currently use Libreoffice Draw, but I have to manually place objects and manually connect them with lines and arrows etc. Thus not a very efficient workflow.

To clarify my need:

I am doing engineering research so I am in look of something more utilitarian than 'pretty', although I like for the figures I create to be soft on the eyes as well. To sumarize, efficiency of use and clarity of the structure diagram are the important factors.
yEd can produce the 'research grade' diagrams that you'd be interested in. 


It can produce nearly all sorts of figures includeing graphs, network diagrams, flow charts, architecture diagrams and block diagrams.
It has a whole wide range of auto arrange feature to rearrange your blocks creating a great professional look for a structure diagram.
It can export diagrams in vetor graphics, which includes PDF, PS, EPS, SVG and so on.
It produces graphml as save file making it cross compatible with graphml coders
Most importantly, it is cross-platform compatable, be it Mac, Windows or Linux.