R IDE/Editors

• R - a free software environment for statistical computing and graphics
• Tinn-R - a free GUI for R language and environment.
  

Data Mining Software

• Weka - an open-source software for data mining
• RapidMiner - an open-source system for data and text mining
• KNIME - an open-source data integration, processing, analysis, and exploration platform
• The Mahout machine learning library - mining large data sets. It supports recommendation mining, clustering, classification and frequent itemset mining.
  
• Rattle - a GUI for data mining using R
  

Clustering

• CLUTO - a software package for clustering low- and high-dimensional datasets
• fastcluster - fast hierarchical clustering routines for R and Python 

Association Rules

• arules - an R package for mining association rules and frequent itemsets
• ARMiner - a client-server data mining application specialized in finding association rules
• A C++ Frequent Itemset Mining Template Library
• Frequent Itemset Mining Implementations Repository
  

Sequence Analysis

• TraMineR - an R package for mining and visualizing sequence data

Social Network Analysis

• Pajek - a free tool for large network analysis and and visualization
  

Spatial Data Analysis

• GeoDa - a free software for spatial data analysis
• CLAVIN - an open source software package for document geotagging and geoparsing that employs context-based geographic entity resolution