Free online peer reviewed journals

Directory of Open Access Journals
Free Medical Journals
Highwire Press freely available journals - many journals not completely free, but it tells you when the free access for articles starts for each journal
Los Alamos National Labs database Physics, Mathematics, Computer Science and Quantitative Biology, orginial public domain science database started in 1991

Agriculture and Fisheries:

Agronomy Journal - all except 2006 issues freely available
Crop Science Journal - all except 2006 issues freely available
Soil Science of America Journal - all except 2006 issues freely available
Acta agriculturae Slovenica - all issues available. Seems two-thirds of content is in Slovenian, the other third in English.
Vadose Zone Journal - all except 2006 issues freely available
Agraarteadus - Journal of Agricultural Science - all issues available - all content in both Estonian and English.
Journal of Environmental Quality - all except 2006 issues freely available
Journal of Natural Resources and Life Sciences Education - all issues including and before 2004 freely available (see 'archived issues')
Agricultura Técnica - all issues available - all articles in Spanish, all abstracts also available in English. Some articles are in English as well as Spanish.
Agricultural Engineering International - all issues available
Agrociencia - all issues available - from 2000 onwards all articles are in both Spanish and English. Before 2000 I don't see any English articles, though I might be wrong.
Agronomy Research - all issues available - Estonian journal all in English.
Annals of Agricultural and Environmental Medicine - all issues seemingly available
Applied Ecology and Environmental Research - all issues available
Biotechnology, Agronomy, Society and Environment - all issues available, only some in English (mostly in French)