After all the positive comments I would like to raise some concern bout some of the not standard R packages. I experienced it twice that there was a serious error in R packages (not a bug, an error in the algorithm). The authors of the first one did not reply, the authors of the second one said they know about it but do not have the time to fix it. I wonder how many esp. of the PhD/postdoc written packages, which I am sure work for their project, are really working correctly in all situations? Not all of them work on their packages as hard and great work as e.g. D. Bates with his lme4 (GLMM) package and it he and users still discover bugs and flaws. I do not want to criticise R, I am using it and I believe that the core packages are as valid as from commercial software (or better) but as I said, I have got doubts with some hardly used ones.
Official R packages (Base and Recommended)
base, boot, class, cluster, codetools, datasets, foreign, graphics, grDevices, grid, KernSmooth, lattice, MASS, methods, mgcv, nlme, nnet, rpart, spatial, splines, stats, stats4, survival, tcltk, tools, utils