mathjax for writting math WELL with LaTex on the web.
DOI stands for "digital object identifier", and is used to provide stable links to scientific articles, among other things. For example... 10.1080/10510974.2013.851096
A nice example of online scientific publishing
gnuplot for high-quality custom plots
inkscape for svg image editing, allong with the older and simplier xfig figure editor. For raster-files, gimp is a great free alternative to photoshop.