Bioconductor - Microarray analysis software library written in R, contributed by a variety of labs Includes Rank Product (RankProd) analysis, Affymetrix (Affy) normalization package
R - Statistics programming language needed for Bioconductor
GeneSifter - Web-based commercial analysis tool with clustering, KEGG pathway, and gene ontology analysis methods
Spotfire DecisionSite - (Windows only) Commercial data visualization and analysis tool well suited to microarray data analysis, with optional functional genomics and statistics features useful for microarray data normalization and analysis
MeV from TM4 - Public domain analysis program with a wide variety of analysis tools including clustering, classification, and statistical analysis methods. Runs under MacOS, Windows, and Linux operating systems. Can be used for analysis of expression data from Agilent, Affymetrix, and spotted cDNA arrays.
SAM - (Significance Analysis of Microarrays) Statistical method for microarray data analysis. Stanford University distributes a Microsoft Excel add-in that performs SAM within an Excel spreadsheet. An excellent implementation of SAM is also available within MeV.
PAM - (Prediction Analysis for Microarrays) Sample classification method which uses the nearest shrunken centroid method. PAM builds a classifier based on a training data set, which can then classify unknown samples. Implemented in R.