ACE-it (Test for copy number impact on gene expression)
CGHMultiArray (Fast two-sample Wilcoxon test for aCGH data)
CGHcall (Calling for aCGH data). Also available from Bioconductor.
CGHregions (Dimension reduction for aCGH data). Also available from Bioconductor.
CGHtest (Statistical permutation tests for called aCGH data)
dnaCplusT (Clustering plus hierarchical testing for aCGH data)
NoWaves (Smoothing waves for tumor aCGH profiles)
PDE test (Partial differential expression test for gene expression data)
PLRS (Modeling the association between DNA copy number and gene expression with constrained Piecewise Linear Regression Splines; by Gwenael Leday)
QCexpression (Quality control plots gene expression data)
Stepwise (Stepwise classification using clinical and genomics data)
WECCA (Weighted clustering for aCGH data)

A presentation of the ideas and some of the maths behind the software  is given at Wessel van Wieringen's site (Analysis of aCGH data)