I recommend the following but I look forward to seeing other approaches (this is my personal approach and by no means the best).
How to Respond to a Review
Every time I respond to reviewers, I create a document. I write a short paragraph thanking the reviewers for their time and state my responses to their comments are below. I copy each reviewer's comments, organized by reviewer (my preference). Beneath each comment, I write a response. If I make a change, I specify where and how I've updated the paper. If I disagree, I state that I respectfully disagree and then elaborate on why. I may choose to include tables, figures, or references in this document that are solely intended for the reviewers.
By doing this, each reviewer can quickly and easily see my responses to their comments as well as my responses to the other reviewers. Where there are similar or duplicate comments, I have similar or duplicate responses to make it easier for the reviewers. I have found this approach to work well---it also helps the editor weigh the totality of the review and my responses.
I send this PDF with the updated paper back in; my hope is that it demonstrates to the editor and reviewers that their comments have been taken seriously.
Sample Format
Authors’ Response to Reviewer Comments
Manuscript: con575r1
We thank the reviewers for their time and helpful comments - their feedback substantially improved this paper. Our responses to each comment are provided below (reviewer comments are italicized in bold). The references listed at the end of this response are intended for all reviewers as cited in our responses.
Response to Reviewer 1...............p. X
Response to Reviewer 2...............p. Y
Response to Reviewer 3...............p. Z
Response to Reviewer 1
Comment 1 Text
Response: Response here to include any required evidence.
Comment 2 Text
Response: Response here.
Response to Reviewer 2
Comment 1 Text
Response: Response here to include any required evidence such as tables, figures, additional results, etc.
Comment 2 Text
Response: Response here.
References
Reference list (if needed) for anything in this Response Document that is solely for the reviewers & the editor. It is not just the references from the paper.