Allen Mouse and Human Brain Atlases: An excellent resource, including very comprehensive ISH data of adult (and for some genes also developmental) mouse brain and spinal cord.
Genepaint: Digital atlas of (mostly) mouse E14.5 embryos. A very good complement to the ABA Developing Mouse Brain atlas
LungMAP: Molecular Atlas of Lung Development, an ongoing NIH funded consortium. The website contains molecular data from developing mouse and human lungs and links to a repository of human lung tissues.
GUDMAP: A molecular atlas of gene expression for the developing organs of the genitourinary tract
GENSAT: A Rockefeller University project mapping the expression of genes in the central nervous system of the mouse, using both in situ hybridization and transgenic mouse techniques. It is a collection of pictorial gene expression maps of the brain and spinal cord of the mouse. It uses EGFP BAC-transgenics and the application of Cre recombinase technologies allows for cell-specific gene manipulation.