If you use Pomelo II, please cite it in your papers. The reference for Pomelo II is Morrissey E, Diaz-Uriarte R. 2009. Pomelo II: finding differentially expressed genes. Nucleic Acids Research, 37, No. suppl_2 W581-W586.
Asterias, a parallelized, web-based suite for the analysis of genomic data, includes applications for class prediction, normalization, survival analysis, aCGH, etc.