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

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)

Databases