g:Profiler : a web-based toolset for functional profiling of gene lists from large-scale experiments. Easy to use web server
KOBAS web server provides KOBAS (KEGG Orthology-Based Annotation System) functionalities on the web. Besides, it has two helpful management uitilites for user with large set of data to analyze.
GSEA :Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states.
ErmineJ : ErmineJ performs analyses of gene sets in expression microarray data. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data