Tools for writing referee reports
I've just taken to returning two documents when reviewing papers:


One is my annotated PDF (created on a tablet) where I can use both margin notes if I want to comment on things, and handwritten notes if I want to draw into a figure or mark up typos. The notes in this document are the smaller comments specific to individual places in the document.
A text file in which I collect the more general, less location-specific comments such as when I discuss the paper's overall structure, how it fits into the existing literature, etc.


This has worked pretty well for me because it allows me to annotate the manuscript right away, and getting back to the bigger items when I've read it all. The only tricky part is that your PDF reader may leave your name in the PDF for all annotations (depending on whether or not you've set it up that way). If you care about your anonymity, you can always edit it out: My PDF reader puts my name in clear text in the .pdf document, and I can just search-replace it by some other string.