Brain Connectivity Toolbox: "The Brain Connectivity Toolbox (brain-connectivity-toolbox.net) is a MATLAB toolbox for complex-network analysis of structural and functional brain-connectivity data sets."
Allen Mouse Brain Connectivity Atlas: "A high-resolution map of neural connections in the mouse brain, built on an array of transgenic mice genetically engineered to target specific cell types."
Brain Architecture Project: "The Brain Architecture Project is a collaborative effort aimed at creating an integrated resource containing knowledge about nervous system architecture in multiple species, with a focus on mouse and human. " Currently includes connectivity and related data and for mouse, human, and marmoset.
Brain Architecture Management System (BAMS): A project developed at the University of Southern California (until 2013). "BAMS is a neuroinformatics environment for handling data from different species. The information that can be stored, processed or retrieved from BAMS is collated from the literature, or consists of experimental data inserted by neuroscientists." If BAMS is not accessible via the main link, legacy connection data from BAMS can be viewed here.
Brain Maps and More: The website of Dr. Larry W. Swanson: A rich source of scholarly publications and other information about the nervous system, including current and previous versions of a rat brain atlas.
General Research Related
Google Scholar: "A freely accessible web search engine that indexes the full text or metadata of scholarly literature across an array of publishing formats and disciplines. (Description from Wikipedia)