I use a number of tools that support my thinking, writing and speaking mainly about innovation.
For quantitative analysis I generally use R and Stata. My workflow might involve both. Sometime I use R for data preparation and subsequently switch to Stata for the econometric analysis. Sometimes I use Stata for data preparation and then I export the data to R for analysis. Occasionally I use Excel or Access for data manipulation. The rather new RStudio makes coding in R a real pleasure. For network analyses I either employ the R-package sna or I use Gephi.
Generally I use MS Word for writing. This is determined by my co-authors rather than by my personal preferences which are clearly towards LaTeX. I recently switched to Sublime Text 3 and to Skim for preview. This is a brilliant and really speedy combination. For my presentations I tend to rely on MS Powerpoint. However, I have recently experimented with HTML5 presentations through RStudio – very light weight and promising.
I manage the papers I read cite through Mendeley with an excellent and automatic export of bibtex-files.