Most effective free software for publication-grade structure diagrams
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.