Genomics & Bioinformatics

Arabidopsis

MATDB (A searchable index of genes and clones, also permits visualization of positional information for BAC clones and single genes)
TIGR Arabidopsis Database
Arabidopsis Functional Genomics Consortium (AFGC) 
Plant Plasma Membrane Database (PPMdb) Database of Arabidopsis plasma membrane proteins with  expression and sequence data.
Arabidopsis Genomics, TAIR

Maize

MaizeDB
Maize links  (from the Maize Co-op at Univ.Missouri)

Rice

Rice Genome Database (Beijing Genomics Institute)
Rice Genome Project (Syngenta)
TIGR Rice Annotation and Informatics
Rice Genome Research Program

Other Plant Genomics Databases

Bioinformatics

TIGR Rice Annotation & Informatics
Comprehensive Online Bioinformatics Service (BioNavigator.com)

Comparative Mapping

GenomePixelizer (A powerful genome visualization tool-downloadable Windows software)
TIGR Brassica Comparative Genomics

Genomics Tools

TIGR genomics tools (a large collection of software tools freely available to the scientific community)
Glimmer (gene finder for Arabidopsis and rice genomic sequence)
BioWeb Pasteur (biological software from the Pasteur Institute)
Queen's University Online Analysis Tools (has great explanations of each tool)
Baylor College of Medicine Sequence Analysis (a fast link to all the types of sequence analysis search categories out there):
ExPASy Proteomics Tools
The CMS Resource (Sequence analysis tools)

Microarrays

Arabidopsis
TIGR microarray resources
WWW Virtual Library Plant Arrays

Proteomics

The Protein Data Bank (3D Molecular data)
The Database of Interacting Protiens (DIP) (catalog of experimentally determined interactions between proteins)
The Protein Information Resource (PIR) (A database of sequences, functional, and structural information to support genomics and proteomics research)
ExPASy Proteomics Tools

Physical Mapping

Texas A&M GENEfinder Genomic Resources (BAC resources for several plant species)

Other

Angiosperm DNA C-Values Database

Techniques/Articles

Nature Genomics (a listing of genomics articles in Nature and Nature Genetics)
Biotechniques Journal (searchable)
Frontiers in Bioscience (links to biology newsgroups and protocols)
Molecular Biology Protocols (claims to be the largest collection of online protocols in the world)
Pasteur Institute (Protocols & databases)

Web Software

Phylogeny Software (some 194 phylogeny packages, and 16 free servers)
Quantitative Genetics Resources (list of resources is maintained as an electronic supplement to our forthcoming two volume textbook on Quantitative Genetics)
Biology WorkBench (a web-based tool for biologists, used to search many popular protein and nucleic acid sequence databases)