This is a system level "engineering diagram" of the mammalian brain. (Why an engineering diagram?) The details in the thalamus and cortex are based on data for the macaque monkey brain, while the rest is common to the rat, cat, and monkey. As far as is known, everything shown at this level applies to the human brain as well (see accuracy). Comments and questions to arobert at interstitiality dot net.
Click here or on the diagram itself for a larger version. It is also available in PDF, SVG, and source format. The diagram was created in OpenOffice Draw. Within this (freely available) program, you can view the systems individually by turning on and off different layers.
The overall organization of the diagram roughly parallels the physical organization of the actual structures, which itself roughly parallels phylogenetic (and to an extent, ontogenetic) development. Some exceptions are made in order to better reflect systems organization or to facilitate an uncluttered spatial arrangement. By and large, the physical arrangement of the brain is such that the lengths of the interconnections between its parts is minimal (to reduce metabolic requirements), and therefore we should expect that arranging a diagram in the same way will result in the fewest number of long lines obscuring the view. Over the course of evolution, however, some connections have grown in importance beyond the ability of the ontogenetic development process to rearrange things, and therefore long fiber bundles and the like are seen in the brain. I have tried to minimize these here, not always possible with only two dimensions to work with rather than three.