The changes I make specifically? What I do is probably a little excessive, but I...
- Copy the default template into Notepad++
- Save that as [Default] template_name
- Copy the modified template into Notepad++
- Save that as [Modified] template_name
- Open them up in DiffMerge to compare the changes, and document them in a separate Notepad++ file
Then if/when the time comes, I reapply those changes if necessary