We examine the nature and temporal trends of science journal publishing, and seek to explain why some journals have higher Journal Impact Factors (JIF) than others. The investigation has implications for how we assess the importance of scientific contributions. National Laboratories run by the U.S. Department of Energy, for example, compare JIF across disciplines, while some academic institutions look at JIF when evaluating publication records. Problematic to these policies are several results, which have long been known in the medical and biological sciences, and are shown here to apply to the Earth sciences as well. In particular, citations are distributed almost logarithmically in any given issue of a journal, and so JIFs say nothing about the actual number of citations acquired by any given paper. In the area of mineralogy and petrology, for example, 25% of articles in a typical issue will capture >50% of all citations that accrue to that issue. For some issues the asymmetry is greater; we use such citation asymmetry to develop a classification for journals as “super elite,” “elite,” “influential,” and “minor.” We also find that JIFs are inherently larger for large disciplines, in part because as the size of a discipline increases (as measured by total papers published), the top journals benefit to a greater extent than other journals. For this and other reasons, JIF cannot be compared across disciplines. A heretofore unknown and disconcerting result is the incredible growth in JIFs for commercially published journals compared to their society-published counterparts—a growth that coincides with the advent of electronic distribution models (e.g., bundling) that were instituted by commercial publishers at the beginning of the 21st century. Journals, which only a decade ago had similar JIFs, and were viewed as being scientifically equivalent, now have very different JIFs. These contrasts may nucleate feedback loops (as authors look to higher JIF journals in which to publish) that threaten the health of society-published journals. Our analysis however, shows that in spite of growing contrasts in JIF, many society-published journals still provide a greater value (JIF/cost) compared to their commercially published counterparts. While we acknowledge that citations and citation rates can be useful tools to compare scientific influence and importance, the results of this and other bibliometric studies cause us to conclude that in the evaluation of science and scientists, it is a grave error to substitute numerical values for human judgment. And if professional societies are to continue to play a significant role in science publication, it is incumbent upon scientists—now more than ever—to send their best works to society-published journals.