We think it would be appropriate to develop a list of existing tools, software and methods that can be used to create or enhance a Reproducible Research Compendium.
Here is what we came up with:

• Sweave -Create dynamic reports (based on LaTeX and R)
• SCons- A part of the Madagascar software package, based on SCons, for managing data processing flows and reproducible computational experiments
• StatDocs-Create interactive statistical documents
• DynDoc-A set of functions to create and interact with dynamic documents and vignettes in R
• MATLAB Report Generator- Automatically generate reports from MATLAB in a wide variety of formats
• Cacher and CacheSweave-R packages for caching statistical analyses and Sweave computations
• Python Tools for RR-Python tools for reproducible research on hyperbolic problems
• Emacs Speaks Statistics-Supports editing of scripts and interaction with various statistical analysis programs such S-Plus, R, SAS and Stata

If you are aware of other tools with a focus on reproducibility, simply write a comment on this post to share it with everyone.

[Updates]

• AMRITA-A system for communicating software-based ideas and information. It operates as a cross between a document preparation system, a computational engine, and a programming language (does not run under Windows)