IDE

• rstudio

Reproducible research tools

• packrat - roughly equivalent to python's virtualenv (isolated package env)
• drake/remake - like GNU make (I think drake is better maintained at this point, but few examples)
• RStudio's projects - at least drops you in the right working directory & ties in with packrat
• Make a package! - higher startup cost, but user installation is trivial
• rocker (R through Docker)

Data import & such

• R.matlab - import .mat files
• data.table - data frames but better, faster, stronger (& fread for flat files)
• Matrix (capital M) - dense & sparse matrices

C/C++

• Rcpp - R <-> C++ interface
• RcppEigen, RcppArmadillo - Interfaces to Eigen & Armadillo linear algebra libraries, respectively

Plotting

• ggplot2

Modeling (easy formula interface)

• lme4 - (generalized) linear mixed models via (Re)ML
• brms - (generalized) (non)linear (mixed) models + more via Stan language
• glmmTMB - (generalized) linear mixed models, probably faster than lme4::glmer() at large sample sizes

Modeling (general-purpose, bring-your-own-cost-function)

• Stan - cutting-edge MCMC, automatic differentiation, hooks into R, python, MATLAB, ...
• TMB - MLE, automatic differentiation, MCMC probably soon?
• nimble - modular modeling/MCMC sampling, autodiff coming

Report generation

• rmarkdown/knitr