The National Center for Biotechnology Information -- PubMed, GenBank, Nucleotide Database, Gene, Gene Expression Omnibis (GEO) Database, Genome, Sequence Read Archive (SRA), Conserved Domain Database (CDD), Protein Database, Blast, and so on. It's a free government website.
The European Bioinformatics Institute -- Part of the European Molecular Biology Laboratory, maintains the world’s most comprehensive range of freely available and up-to-date molecular databases.
EMBL-EBI provides freely available data from life science experiments, performs basic research in computational biology and offers an extensive user training programme, supporting researchers in academia and industry.
The SIB Bioinformatics Resource Portal -- which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.
KEGG: Kyoto Encyclopedia of Genes and Genomes, is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
The Protein Databank -- Protein 3D structure database, is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. These are the molecules of life that are found in all organisms including bacteria, yeast, plants, flies, other animals, and humans.
The Universal Protein Resource -- a comprehensive resource for protein sequence and annotation data, a combination of Swiss-Prot,TrEMBL, PIR-PSD and iProClass.