While algorithms and methodologies to study uncertainty in the Earth Sciences are constantly evolving, there is currently no free integrated software that allows the general practitioners access to these developments. This paper presents SGEMS-UQ, a plugin for the SGEMS platform, that is used to perform distance-based uncertainty analysis on geostatistical simulations, and the resulting forward transfer function responses used in subsurface modeling and engineering. A versatile XML-derived dialect is defined for communicating with external programs that reduces the need for ad-hoc linking of codes, and a relational database system is implemented to automate many of the steps in data mining the spatial and forward model parameters. Through a graphical user interface, one can map a set of realizations and forward transfer function responses into a multidimensional scaling (MDS) space where visualization utilities, and clustering techniques are available. Once mapped in the MDS space, the user can explore linkage between simulation parameters and forward transfer function responses using a module based on a SQL database. Consideration is given to the use of software engineering paradigms and design patterns to produce a code-base that is manageable, efficient, and extensible for future applications, while being scalable to work with large datasets. Finally, we illustrate the versatility of the code-base on an application of modeling uncertainty in reservoir forecasts for an oil reservoir in the West Coast of Africa.