The latest release of JBrowse is always available on GitHub.  Download it here.

Then follow the tutorial instructions for prerequisites (CPAN/Bioperl), installation and testing.

Once your JBrowse is up and running, the JBrowse Configuration Guide on the GMOD wiki is the comprehensive reference for the many ways to display your data with JBrowse.

For developers: 
See the developers page for details about how to set up a development environment for working on JBrowse code.

Citing JBrowse:
If you use JBrowse in a project that you publish, please cite the most recent JBrowse paper, which is here in Genome Research.