FlyAtlas - The Drosophila gene expression atlas. This database gives information for the question "Where is my gene of interest expressed/enriched in the adult fly?" For each gene and tissue you get the mRNA SIGNAL (how abundant the mRNA is), the mRNa ENRICHMENT (compared to whole ones), and the Affymetrix PRESENT CALL (out of 4 arrays, how many times it was detectably expressed).
METscout - A MySQL relational database linkng biochemical pathway information with 3D patterns of gene expression determined by robotic in situ hybridization int he E14.5 mouse embryo.
Mouse Genome Informatics (MGI) is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.
NHPRTR - Non-human Primate Reference Transcriptome Resource. Developed in 2010, Next Generation SEquence complete transcriptomes from mutiple non-human primate species
OikoBase - A curated genome expression database of Oikopleura dioica. Information on ESTs, transcripts, proteins and genome-wide expression profiles.
OnTheFly - A database of Drosophila melanogaster transcription factor DNA binding specificities
WDDD - Worm Developmental Dynamics Database. Quantitative information about cell division dynamics in early Caenorhabditis elegans embryos when each of all essential embryonic genes is silenced individually by RNA interference (RNAi).
WormBase is an international consortium dedicated to providing accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes
ZInc - Zebrafish Insertion Collection. Database on zebrafish mutations. A searchable interface for determining if a specific gene has been mutagenized by proviral insertion.