Here's a quick table of what I think are the most useful apply-style commands in R: FunctionInputOutputBest forapplyRectangularRectangular or vectorApplying function to rows or columnslapplyAnythingListNon-trivial operations on almost any data typesap...

Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).