I'd suggest using a modelling tool to perform Model-based testing; we use one called DTTDirect-to-test (DTT) at our workplace. Basically, you can set up a path through the application and specify what should vary based on what configuration files, proving therefore that you've covered every configuration file option (usually a cluster of nodes at the beginning of the model) and every path through the application, and let the tool generate the test cases from that. It's not a spreadsheet, but it can be easier to show people outside your department a graphic than a spreadsheet anyway.