R & Weka

Weka is a great resource for data mining and machine learning.  You can get a lot done with the standalone GUI workbench, but sometimes you need to use it as part of a script in a custom R analysis pipeline.  Yes, you could create a shell script that makes use of the Weka command-line tools, and invoke said script from R using a 'system' call, but that could get out of hand really quickly.