This is another of the aspects of doing science that nobody explicitly teach you. The basics are pretty simple to explain (just respond to everything and point by point). You start by mimicking what your mentor does, how other co-authors respond, and how other people respond to your reviewers. But after seeing different co-authors at work, and specially now that I saw a lot of responses from different people as an editor, there are bad responses, good responses, and those so good, that make your paper fly to the publication stage. Why? The little differences.
1) Be concise (i.e. give a lot of information clearly and in a few words). You can spend some time in formalities and a “thank you” part and a “highlighting the strong points part” is important, but make your case quick and personal. Don’t thank reviewers for “enhancing the paper” because you have too. Thank them for pointing out A or B, which really made a difference. If comments were minor, its not necessary to make a big deal with empty words because you want to be concise. Being personal and not using pre-established “thanks you phrases” helps connecting with the reviewer and sets his/her mood for reading the rest. Also, always briefly highlight the positive things. Editors are busy people, if a reviewer are supportive or partially supportive, bring that up in the response to the editor to put him back in context.
2) Following with conciseness, show that you care about the science. If you did a good work, reviewers do not know your data/analysis as well as you do, so make them trust you by providing details on the decisions you made, and back up all your claims with data and references, not only in the Response to Reviewers, but also in the edited paper. This seems obvious, but I’ve seen several “we don’t agree with this change” without a proper justification.
4) Number your responses. that allow you to refer to previous responses, and avoids repetition. Nobody wants to hear the same justification twice. If your reviewer is not tidy (e.g. do not separate main concerns, from small comments), you should be. Your responses should always flow and for example, you can summary main changes first, and then refer to it when brought up by the reviewer in the middle of other in-line comments that deal with smaller wording issues.
5) Put the focus of the review on the ms, not on the R to R. That means that other than in particular cases you don’t quote the changes in the response, but refer to the lines where the changes are. BUT the real pro-tip is that you highlight the changes in the new ms. Track changes are burdensome and require software specific, but using a different color (I personally like using blue font because red is too contrasting) for the changed sentences in the new ms is a big help for reviewers. This allow both, a smooth read of the full paper, and makes it easier to find the new passages.
Any other tip you use?