For the reasons described in this post I tend to separate in different commits those changes that alter functionality from those that are refactorings.

Sometimes I refactor before making my changes, and sometimes I do it afterwards. In any case I try not to mix a change in the functionality and some refactoring in the same commit. That way, in retrospect, it's easier to me to understand each commit: the ones related to changes in functionality have simple, easy to understand diffs, and the ones related to refactorings have messy diffs but at least I know that they don't change any functionality.