How to Decide Where to Submit a Manuscript in Physical Oceanography

Journal choice should be based on several considerations:
    1. Does the journal exist in electronic form?  Increasingly, leading journals in physical oceanography are received by libraries only in electronic form, and readers are reluctant to make a trek to the library to dig out a single paper that might be needed as a hard copy.  Course instructors, journal clubs, and student seminar series disseminate reading material electronically and will simply not assign reading that is inconvenient.   If you want your work to be read, it needs to be electronic, and it will have even more success if it's open access.
    2. Can libraries at small institutions afford to subscribe to the journal?  As journal prices rise, libraries increasingly must cut subscriptions.  A number of studies have shown that commercial publishers are collecting the lion's share of library subscription budgets, but that articles in commerically published journals garner a comparatively smaller number of citations.   Thus as a rule of thumb, it's usually better to publish in journals put out by AGU, AMS, or other societies (e.g. the Journal of Marine Research, published by the Sears Foundation), rather than commercial journals.  In physical oceanography, this means being wary of Progress in Oceanography, Deep-Sea Research, Dynamics of Atmospheres & Oceans, the Journal of Marine Systems, and Ocean Modelling (published by Elsevier), and Climate Dynamics and Boundary-Layer Meteorology (Springer-Verlag).  Of course, some commercially-published journals fulfill specific niches that the society journals do not readily address.
    3. Is the journal indexed by the ISI Web of Science?   Increasingly, researchers track down literature that is relevant to their own studies by running a simple keyword search.  If the journal isn't indexed, then the articles may not be located.  Journals in physical oceanography that aren't indexed include, for example,  Oceanography (published by The Oceanography Society), EOS (the AGU newsletter), and Marine Geodesy.  These unindexed journals may have other virtues, but the trade-offs of publishing in them should be weighed carefully.
Examples of non-profit journals relevant to physical oceanography:
American Meteorological Society:  Journal of Physical Oceanography, Journal of Climate, Journal of Atmospheric and and Oceanic Technology, Bulletin of the American Meteorological Society, Journal of the Atmospheric Sciences.
American Geophysical Union:   Geophysical Research Letters, Journal of Geophysical Research (Oceans).
European Geophysical Union:  Ocean Science.
Yale University (Sears Foundation):  Journal of Marine Research.
Cambridge University Press:  Journal of Fluid Mechanics.

Some studies on journal costs:
Economics:  http://www.econ.ucsb.edu/%7Etedb/Journals/jeprevised.pdf (Bergstrom, Free Labor for Costly Journals?)
Biomedical research:  http://www.wellcome.ac.uk/assets/wtd003182.pdf (The Wellcome Trust, Economic Analysis of Scientific Research Publishing)
Marine science:  http://research.dils.tku.edu.tw/Joemls/41/41-3/315_323.pdf  (Marine Science Journal Prices:  A Case Study, Journal of Educational Media & Library Sciences, 2004)


Other resources:
UC San Diego blog:  New Directions in Scholarly Publishing 

Sarah Gille, November 2006, November 2008 (drawing on information from scholarly communications talks by Ted Bergstrom and Lee C. Van Orsdel, among others).