Biology

Genes

Genetics

Specifically regarding the founder of Genetics, one must check the resourceful MendelWeb. An English translation of his 1965 paper, as well as an exhaustive discussion of the genuinity of his work, are available online.
Then, a history of Genetics from 1900 to 1953, the Barbara McClintock papers,

Arabidopsis

Lehle Seeds makes for the best entry point for Arabidopsis thaliana in the Web, for its excellent resource page hosting for the visitor a enviable collection of links (if not structured) to "everything Arabidopsis".

Just in case, in my site you can find a page directing to my scholar texts (in Portuguese), one of them dealing with the practical use of Arabidopsis thaliana for teaching.

OMIM

Online Mendelian Inheritance in Man, a vital reference both for fundamental and for clinical research in Human Genetics, that once existed as heavy books, but now at the click of the mouse. All known phenotypes, pathological as well as normal, are collected and organised for the use of the scientific community. An obligatory link with genomes research, human and others.

Molecular Biology

Molecular Biology protocols sites

The Molecular Biology today e-zine
The Cell & Molecular Biology Online site
One of the sections in the Comprehensive Protocol Collection in Dartmouth College
The Technical Tips Online at BioMedNet
One section in the Protocols Online, at Pedro's page
Orbigen features many protocols along many useful links and services, worth a close look.
The Wiley Bioprotocols site
The resources page from Lehle Seeds (described in the Arabidopsis section below).
Bioprotocols
Hot molecular methods
Software at INRA (France)
The Biotechniques journal has an exhaustive site, as would be expected.
A PDF manual on biosafety written in Spanish, Bioseguridad en laboratorios de Microbiologia e Biomedicina.

Genomes

The best starting point: Genome Database
An index to genome papers online
Searching the GenBank database with Entrez
A database that made History because it was set to be open to all users: dbEST and the Genome Sequencing Center
Genescope, the human genome foremost.
Arabidopsis Genome Initiative, and Arabidopsis thaliana gene classification site. Check out further genome links at the Plant Genome and Information Center
The Molecular systematics homepage
ExPaSy Proteins on the Web.

Microbiology e Mycology

An excellent microbiology portal:

Mushrooms

Mycology Resources, systematic resources at Mykoweb (a huge site to explore!) and Mycologue Publications, Canada.
Mycoinfo, internet journal and links site. The Fungi systematics page at the Tree of Life site (referred below) supplies a huge collection of links.
Truffle.org is a multilingual site specifically dedicated to truffles. Excellent layout and wide coverage.
The British Mycological Society, and its resources page.
The North American Mycological Association and the Oregon Mycological Society.
Cornell Center for Fungal Biology and their biodiversity project database. The Univ. California at Berkeley is "filling the gaps" in a very instructive systematics site.
Systematic Mycology (and Botany).
Dr. Fungus is quite medically-oriented but offers a lot.
Mycological molecular methods (University of Tennessee)
Fungi at Natural Perspective.
Fungi systematics at the National (US) Biological Information Institute. See also a key for the Fungi kingdom and try this search at the US Dept. of Agriculture.
Mushroom expert, with online determination keys (for example those for Boletus spp.)
Mycology sites in Spain: Hongos y setas (general information site), other links
Other sites: Especies con usos non-maderables (Mexico), Brazil fungi recorded by Batista et al., images of boleti (Italy) and Shunsoft, home to taxonomy software.

Mycorrhizas

Online Mycorrhizal Information Exchange, a collective mycorrhizal website.
A reference database focused on mycorrhiza publications, built and maintained by David Sylvia, is available free of charge and can be very helpful.
Mycorrhizas WebPage is a very resourceful site on methods and bibliography on mycorrhiza, set up by Mark Brudrett.
If you wonder about ectomycorrhiza molecular ecology, Tom Bruns lab may satisfy some of the curiosity.
One of the databases coming out from the Molecular Biology efforts is MycorWeb
A growing online database for ectomycorrhizal morphotypes
Ectomycorrhizal mushrooms. See also an illuminating online account of a ectomycorrhizal mushroom successional series in a pine plantation in Surrey, England.
An observatory of microorganisms in arid ecosystems.
A FAO site on inoculation of forest species with mycorrhizal fungi
A list of forest research centres in Spain

Ecology and Evolution

The Tree of Life, a serious web project compiling the diversity of living organisms
World Data Center for Microorganisms (another huge thing!)
The Smart Office glossary has some reference definitions mostly related with organismal evolution.
A good resource on life forms and their classification.
An introduction to phylogeny
The 1978 Whittaker system of classification, Botany-oriented.
Coalescent theory and applications
Of the late Stephen Jay Gould.

General

Botany

Just the links, not that much of a descritption.

At the SeaWIFS project satellite images page one can find beautiful depictions of the photosynthetic activity in land and sea.
And check out the Global Diversity Map for vascular plants by the Biomaps Project at the Bonn University Botanical Institute.
Online Vegetation and Plant Distribution Maps. A Cartography links site is also available.

Internet Directory for Botany a good jump site (lots of links). See for example the vascular plants page.
GRIN taxonomy, excellent for looking up each species.
Vascular plant family nomenclature, by James Reveal.
Families of Flowering Plants Watson & Dalwitz.
The Treezilla project (phylogenetic reconstruction for seed plant families).
Plant family ID.
Species 2000, one of the mirrors of the main page, some with useful checklists like the one in fishbase.
Example of a query on Plants National Database, another on Inference find, and another on fishbase dynamic checklist.
WWW Virtual Library: Botany
National (US) Plants Database
Gymnosperm database
Internet Resources for Botany and Plant Ecology one of the links pages by Ann Throckmorton, Westminster College, Pennsylvania.
Flowering Plant Gateway gigantic site.
Search names from Kew.
Taxonomy of Flowering Plants.
Univ Catania Dicots (Italy).
Phylum, Magnoliophyta and Family directories, Univ. West Madison.
Plant fossils and evolution.
Vascular Plant Families and Genera at Kew.
Example of search at University of Bonn Botanik Department.
Woods.
Dendrology (US).
Seed plants at Berkeley, at Cornell.
Kapili.
Quercus systems, Quercus at TreeWeb and Quercus suber Network.
Phylum Magnoliophyta Good links list.
The Herbweb a list for useful plants.
The Herbage Botanical Database focuses on ethnobotanical uses, contains over 29,000 species.
Euro+Med Plant Database
Database of Plant Databases.

Envirolink:
Global, Alleles list, Species list, same, non US, BigFiles, TreeWeb

CalPhotos: images.
Images and Descriptions of Flowering Plant Families.
Image Gallery for Vascular Plants, searchable.
Horticopia (images)
Angiosperm images from Albion College.

The Royal Horticultural Society Site, for example its page dedicated to trees and shrubs.
A site on agricultural history

Famine foods by Newcrop.

Tree links:
FAO Forestry Department
Le Bois (France)
A forest genetics laboratory in France (INRA)
Ohio Products
Keslick & Son, Modern Arboriculture & LandscapeMaintenance, highly watchful on everything that relates to environmental issues in tree growth and maintenance.

A Compendium of plants for exotic gardens.

Sierra Nevada Edible Plants (by family)

Fauna e flora do montado (Portugal)

Literature sources

All things Biological (links and usenet discussion groups) for one to have in the favourite bookmarks set: The BioSciences Site. At Harvard University one can look at the Golgi BioPages and most certainly some useful links will come up. Another general-purpose site, with thoughtful and well-written articles on all fields of Biology, is the Life and Earth Sciences sections at about.com.

Biomedicine-oriented users have all reasons to become members of the BioMedNet.

PubMed has the largest biomedical literature database online. It forms the basis for searching for so-called Alternative Medicine.

The old UnCover Reveal resource has teamed with Ingenta to make an excellent reference resource.

The Biochemical Genetics site from the University of California at San Diego is an excelent reference in the field.

To have your thesis or other communications published online, connect to the Yellow Index for this and for much more.

The Kluwer Academic Publishing Information Service is worth the visit.

Software

The DELTA system (DEscrition Language for TAxonomy) is becoming evermore the standard means for classification and identification of life forms.

MEKA online identification programme.

Treeguide.