Writing papers and making figures is and always will be a big part of what scientists do. Many of us use open source software, such as Fiji, to process images however the figure is often finalised in commercial software - typically from Adobe. Needless to say neither Photoshop nor Illustrator are designed to make scientific figures.
Two groups have recently introduced plugins that leverage the tools available in ImageJ/Fiji to make scientific figures. Both tools are made by scientists introducing innovative concepts specifically designed to make scientific figure making easier and more controlled.
Mutterer, J. & Zinck, E. (2013) Quick-and-clean article figures with FigureJ Journal of Microscopy, 252 (1), 1365-2818 <doi:10.1111/jmi.12069>
Aigouy B. & Mirouse V. (2013) ScientiFig: a tool to build publication-ready scientific figures Nature Methods, 10, 1048 <doi:10.1038/nmeth.2692>
Each tool is available in Fiji through its own Update Site.
Finally the OMERO team is also rolling out a Figure making plugin showcased here http://www.youtube.com/watch?v=anJPPx7uoUM.
Making figures will never be the same.