Array File Maker 4.0 - B.J. Breitkreutz et al. (Samuel Lunenfeld Research Institute, Mount Sinai Hospital) have created a series of programs that manipulate and manage DNA microarray data. Given a database of expression ratios, AFM 4.0 generates input files for clustering, helps prepare colored figures and Venn diagrams, and can uncover aneuploidy in yeast microarray data.
AMIADA is an integrated computer program for organizing, exploring, visualizing, and analyzing microarray data produced by X. Xia (University of Ottawa). It features an EXCEL-like user interface and performs data transformation, principal component analysis, a variety of cluster analysis and extensive graphic functions for visualizing expression profiles.

Cluster: Perform a variety of types of cluster analysis and other types of processing on large microarray datasets. Currently includes hierarchical clustering, self-organizing maps (SOMs), k-means clustering, principal component analysis.Hierarchical clustering methods described in Eisen et al. (1998) PNAS 95:14863.

ScanAlyze [Download]: Process fluorescent images of microarrays. Includes semi- automatic definition of grids and complex pixel and spot analyses. Outputs to tab-delimited text files for transfer to any database. Written by Michael Eisen. 

OligoWiz - provides intelligent design of oligonucleotides for DNA microarrays. See: Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays. Henrik Bjørn Nielsen, Rasmus Wernersson and Steen Knudsen. Nucleic Acids Research, 2003, 31: 3491-3496.