Be polite – but not over-polite
It is important to address the reviewers in a polite manner, even if you totally disagree with their comments. However, you should not be over-polite. I once edited a point-by-point response to a set of reviewer comments in which the author prefaced and ended each individual response with an expression of gratitude.
Something like this:
Thank you very much for your excellent comment.
[Response to specific comment]
Thank you very much again.
This excessive politeness might give the impression that the author is trying to charm the reviewer, to get the paper accepted by being polite rather than by addressing what the reviewers consider to be its flaws.
What to do when two reviewers ask for opposite things
Okay, so you get the reviewer comments back from the editor and Reviewer 1 feels that the Introduction lacks detail. Reviewer 2 on the other hand thinks it is too long. What to do? In such instances it is best to ask the editor for advice. After all, it is he/she who has the final say as to whether or not your paper is accepted. You can then refer to the advice you received from the editor when writing your responses to the conflicting reviewer comments. (Note: If the editor bothers to read through the reviewer comments carefully they may flag the problem in the decision letter.)
Dealing with comments you don’t understand
Sometimes peer reviewers will make comments that you don’t understand; on other occasions it may be unclear whether they are just commenting on something or want you to make changes. When this happens I would advocate a policy of openness. Explain to the reviewer that you don’t understand what they mean, or what they are asking you to do. At the same time, it is worth writing responses based on what you suspect the reviewer may be getting at:
I am afraid that I am unclear as to the point you are making. If you are saying that the sample was too small, I would respond that [...]. If instead you feel that the outcome measure was flawed, I would argue that […].
Engage the editor as an adjudicator
You and a reviewer are unable to agree on a particular point. The reviewer repeatedly requests a specific change and you reiterate your opposition to it. After several rounds of review, agreement is no nearer. In such circumstances it is advisable to raise the issue directly with the editor. Present your argument to them as convincingly as you can and let them decide what should be done. There is no guarantee that you will get the outcome you hope for, but at least you will no longer be bashing your head against a brick wall.