I have something like Brodmann Areas in mind, but any complete list of cortex regions would do. I'm primarily interested in human brains here. Ultimately I'd like enough information to be able to build an NxN matrix containing boolean "innervates" entries. Numbers representing an "innervation strength" would be great too.
One of the primary tools used to map functional and anatomical connections is diffusion tensor imaging (DTI). Unlike the more often used T2-weighted images, DTI allows researchers to image white matter tracts directly.
The data from the HCP is available for free to researchers, but you need to apply for access. See their website for details.
You might be very interested in a paper by Felleman and Van Essen (1991). In the paper, they analyze the connections between many cortical areas, and create a database to store the connection values. They also have some interesting things to say about hierarchical connections and cortical layers.
Currently, no such high-level maps based directly on human cortex exist (as far as I can tell). The closest model organism for which high-level maps exist is the macaque:
In 1991, Felleman & Van Essen published the first extensive analysis, which includes a noteworthy connection diagram (see p. 30).
In 2010, IBM (Modha & Singh) published what appears to be a complete set of connection diagrams.