Psychologist Henry L. Roediger III gives some excellent advice for reviewing journals papers (two word summary: be nice!). Though a psychologist, his twelve tips should have applicability for all academic disciplines. An excerpt from his introduction follows:
Many critical skills needed for becoming a successful academic are typically not taught in graduate school, at least not in any formal way. One of these is how to review journal articles. Few students coming out of graduate school have much experience reviewing papers, and yet, at least for those students continuing on in research, reviewing is a skill that will be increasingly critical as their careers develop. In fact, being a good reviewer can greatly help a career. If a young psychologist becomes known as an excellent reviewer, he or she may be selected as consulting editor, then associate editor, and then perhaps the primary editor of a journal.