World wide technological advancement has brought in a widespread change in adoption and utilization of open source tools. Since, most of the organizations across the globe deal with a large amount of data to be updated online and transactions are made every second, managing, mining and processing this dynamic data is very complex. Successful implementation of the data mining technique requires a careful assessment of the various tools and algorithms available to mining experts. This paper provides a comparative study of open source data mining tools available to the professionals. Parameters influencing the choice of apt tools in addition to the real time challenges are discussed. However, it is well proven that agents aid in improving the performance of data mining tools. This paper provides information on an agent-based framework for data preprocessing with implementation details for the development of better tool in the market. An integration of open source data mining tools with agent simulation enable one to implement an effective data pre processing architecture thereby providing robust capabilities of the application which can be upgraded using a minimum of pre planning requirement from the application developer.