My current state is a mixture of spreadsheets, wikis, documents, and dated folders for my input/configuration and output files and bzr version control for code.

I am relatively new to programming that requires this level of documentation, and I would like to find a better, more coherent approach.

update (for clarity):

My inputs are data used to generate configuration files with parameter values and my outputs are analyses of model predictions.

I would really like to have an approach that allows me to associate particular configuration(s) with particular outputs, so that I can ask questions of my documentation such as "what causes over/under estimates?" or "what causes error 'X'"?