I use LaTeX and R (on Slackware GNU/Linux) to achieve reproducible research.

Current setup

Typesetting/Referencing: LuaLaTeX/XeLaTeX, biber, biblatex, biblatex-apa, memoir

Statistics: R, knitr

R Packages: RMySQL, psych, reshape2, ggplot2, lmer

Editor: Emacs/ESS/AUCTeX