The online botanical literature can be divided into two categories.
Much public domain botanical and horticultural literature is being digitised. The big repositories are Internet Archive, Google Books, Gallica (at the Bibliotheque Nationale de France), Botanicus (at Missouri Botanic Garden), the Digital Library of Real Jardín Botánico of Madrid, and the BioLib Online Library of Biological Books.
As of 4th December 2008 Internet Archive has 2221 volumes tagged as addessing the subject of botany, plus many other volumes tagged as being about floras, forestry, gardening, horticulture, paleobotany, plants and trees. (No doubt a judicious choice of keywords will find additional volumes.) Essentially all volumes are available as PDF files. Internet Archive also indexes some of the books held by Google Books.
more keywords: perennials, flowers, wild flowers, floriculture
As of 21 February 2011 the Botanicus project at Missouri Botanic Garden has 4229 volumes, representing 962 titles. These are mostly public domain works, but runs of later issues from some journals such as Annals of the Missouri Botanic Garden, Novon, Rhodora and Sida are included. Not all volumes are available as PDF files, but PDF files have often been added for volumes previously only available in other formats.
As of 15 February 2012 the Gallica project at the Bibliothèque nationale de France has 1923 documents tagged as addressing the theme of botany (botanique) and 553 documents tagged as addressing the subject of plants (plante). Other works can be found under other subject headings (e.g. floraison). All volumes are available as PDF. In addition to its own collections Gallica also indexes smaller collections at the University of Strasbourg and the University of Paris V. The former does not provide works in PDF or other downloadable format.
As of 21 February 2011 the Digital Library (Biblioteca Digital) of the Real Jardín Botánico of Madrid has 5604 volumes representing 2391 titles (2187 books and 204 periodicals). (The Digital Library indexes many works, especially recent journal issues, hosted elsewhere, and it is not immediately obvious whether the figure of volumes is for hosted volumes, or indexed volumes.) This includes many works related to the botany of the western Mediterranean region. A considerable number of open access journals are indexed. Works are available in PDF format, but there is a restriction, whether intentional or otherwise, on the number of pages that can be downloaded in a single PDF file).
As of 24 January 2009 Google Books has 620 volumes tagged as addressing the subject of botany, and 491 tagged as addressing the subject of plants, with some overlap. Other works can be found under other subject headings. Volumes are available as PDF.
As of 15 November 2008 the BioLib Online Library of Biological Books has 2005 volumes categorised under the subject of botany.
Smaller numbers of works can be found on a variety of sites, including Project Gutenberg, the Center for Retrospective Digitization, Göttingen (GDZ), the Biblioteca Digital de Botânica at the University of Coimbra, the University of Georgia, the University of Wisconsin Digital Collections, the Smithsonian Institution Digital Library, the US National Herbarium, a Czech site (from the library of the Archbishop's palace at Kromerí), Humboldt University, Berlin, the University of Hamburg, the Braunschweig Digital Library, Berlin-Dahlem Botanical Garden and the Rain Forest Restoration Initiative.
The Biodiversity Heritage Library site indexes a subset of Internet Archive and now also Botanicus. In some ways it is a more helpful index; it collects the multiple volumes of a single work or journal together in a single record, and search results aren't cluttered with records for other topics. However it lags the internal indices, and doesn't cover all the botanical material in Internet Archive. Open Library is another indexing service.
JSTOR provides a variety of historical as well as more recent journals. Unfortunately access to this is paywalled. Journals available include
SpringerLink sometimes make access to individual journals available to non-subscribers.
The University of Rioja Dialnet site provides copies of many journals and theses.