Ensembl

Ensembl is a collaborative effort of the EMBL- EBI and the Sanger Institute to create automatically annotated eukaryotic genomes. It provides an excellent data source on genes, transcripts and their translation products of a large number of eukaryotes. Each datum is extensively annotated and cross-references with related data.

Ensembl can be accessed via a sophisticated, yet relatively easy to use web interface. However, the true value of Ensembl comes from the fact that it has an open read-access SQL interface. Therefore, you can easily use any SQL-savvy client for complex queries. In addition, you can download complete genomic datasets as SQL dumps and import them into an SQL database such as MySQL or Postgres.

The one drawback of Ensembl is its rather convoluted and complex (and not perfectly documented) entity relationship model.