If 
was a band, and if that band had a greatest hits album, and if the album featured R commands instead of songs, then the following commands should be counted among the greatest hits (or the most obscure hits).
- windows(record=T) #place this near the top of your script to record all charts; enables scrolling through and compare charts with page up and page down
- oldpar <- par(no.readonly=T) #assign default graphical parameters to an object, to be called back later with par(oldpar)
- windowsFonts(Garamond = windowsFont(“TT Garamond”)) #add a new font family to the standard database
- file.choose() #allows you to choose a file interactively instead of specifying the path and file name in quotes
- describe() #a better alternative to summary(); from library(psych)
- qq.plot() #plots a quantile-comparison chart with confidence bands; in library(car)
- prplot() #a function in library(faraway) that produces partial residual plots
- Make.Z() #normalizes all variables in a data frame, available in library(QuantPsyc)
- ci.rc() #calculates a regression coefficient confidence interval, in library(MBESS)
- hccm() #another from library(car); calculates heteroscedasticity-corrected covariance matrices for unweighted linear models
- lmer() #a function in library(lme4) that fits linear mixed models
- identify() #use this function in library(graphics) to label points in a scatter plot