Pet peeve: In a number of research papers, I see that the bibliography is sorted by author name. The problem with this sorting is that it supports a single function --- to check how many times a particular author is cited in a printed paper as the first author. Unfortunately, when bibliographies are sorted in this fashion,  it becomes very difficult to look up where in the paper that particular entry was cited. If you order the bibliography by the order in which it is referred to in the paper, it becomes much more easier for the poor reader to look up where and why a particular entry was cited in your paper.

IMO, the second function is much more important than the first. So, my plea to the authors: Please, order the bibliography by the order of reference.