How to organize the referee report of a paper?
I organize my reviews in the way that I would like to receive them, sorted from most important from least important.  My general structure is:


First, I summarize my understanding of the the key ideas and contributions of the paper.
Next, I give my judgement and main reasons for this judgement.
Third, I have a "Major Issues" list of other scientific problems that I think absolutely must be addressed before publications
Finally, I give a "Minor Points" list of nitpicking, language issues, typos, etc.


The first two sections show that I have understood what the authors are trying to say, and the big picture issues.  The third gives the contributing factors, but tries to make it clear that fixing these without fixing the big picture issues won't change my basic judgement (if that judgement was negative).  The final is things that will improve the paper but aren't really affecting my judgement.