I have written an number of pieces of software. Mostly for the analysis of microarray data. I am currently a BioConductor contributor. Source code repositories for many of these can be found on my GitHub profile:
Program Description Where to get
RMAExpress A program for generating RMA expression values for Affymetrix GeneChip microarrays. Source code is available licensed under the GPL. Pre-compiled binaries are available for Microsoft operating systems. May also be built successfully on Linux operating systems. Consists of three separate programs: RMAExpress which is a GUI program, RMAExpressConsole runs on the command line and RMADataConv for certain file format conversions.
affy An R package for low-level analysis of Affymetrix GeneChip data. Provides some pre-processing facilities and methods for examining probe intensity data. Joint work with Rafael Irizarry, Laurent Gautier and others. Includes the R function rma() for computing RMA expression values and also the base implementation of the quantile normalization algorithm.
affyPLM An R package providing methods for fitting probe-level models to Affymetrix GeneChip data. Provides additional pre-processing methods beyond those in the base affy package. It provides quality assessment tools for GeneChip data such as the figures at
affyio This R package provides parsers for Affymetrix file formats based upon available documentation.
BufferedMatrix This is an experimental R package which implements an out of memory matrix for dealing with large datasets, Buffers are used to provide some level of speed up. Currently sources are stored in the BioC svn archive. Some simulation results are here.
BufferedMatrixMethods This is an experimental R package which uses the BufferedMatrix structures for microarray processing. Some simulation results are here.
preprocessCore This R package contains a number of low-level preprocessing routines. The interface to this code is both at the C-level and the R-level. Both affy and affyPLM depend on this package. You can find a discussion of runtime performance of the PLM fitting code here. Other simulation/testing results for preprocessCore are stored here.
AffyExtensions (Defunct) An R package which provides additional, but sometimes experimental, functionality for the analyzing Affymetrix data. Has often served as a place where functionality is developed that is later moved into the affy and affyPLM packages. Because of possible instability (although usually everything is fine) this remains outside BioConductor although it supplements and depends on many of these packages. AffyExtensions
SMA (Defunct) Statistics for Microarray Analysis (SMA) was an early R package for pre-processing/normalization of cDNA and other two color microarray data. At this point (Jul 2006) it is mostly defunct and has been superceded by software in BioConductor. This package was joint work with Sandrine Dudoit and Jean Yang. Also see CRAN

Some notes/FAQ on the software

Why do my MAS 5.0 values differ? explains the differences between the MAS 5.0 implementation in BioConductor affy package and those that you might get from Affymetrix MAS 5.0 software.
Some FAQ about computing the RMA expression measure has details about computing the RMA expression measure using currently available software.