Im not sure this is exactly what you want, but newer version control tools like mercurial and git have features specifically for handling cases like this. In the case of mercurial their patch queue features are very useful.

For all of you who are stuck on centralized version control systems take a moment to learn either mercurial or git, you wont look back and youll be a much happier person. There has been a paradigm shift in version control going on almost silently in our industry and its something you should know about.