BradleyTerry2: an R package to specify and fit Bradley-Terry models, including models where abilities are related to explanatory variables through a linear predictor.
gnm: an R package for specifying and fitting generalized nonlinear models.
qvcalc and Kuvee: an R package and an online calculator which compute more useful standard errors for group and factor effects in linear, loglinear, logistic, etc. models, overcoming the usual "reference category" problem.
relimp: an R package for inference on the relative importance of effects in statistical models.
PDFjam, a small collection of shell scripts that provide a simple interface to some of the functionality of the pdfpages package for pdfLaTeX. Facilities include n-up imposition, page rotation, reflection, trimming, selection of pages, and many more. Part of TeX Live, and available separately also as a stand-alone package for various operating systems.
Older software, still available here but no longer maintained:
brlr: an R package for bias-reduced logistic regression using penalized maximum likelihood.
CGIwithR: an R package which allows R to be used straightforwardly as a CGI scripting language (Unix only)
tapiR: tools for accessing and organising UK House of Commons division data in R, and associated datasets.