I find setuptools works great for packaging whole apps with HTML/JS/CSS. You can put these data files in your Python package directory, list them in MANIFEST.in, and set 'include_package_data=True' in setup.py. Then you can reference them in your code relative to __file__. And you can include a run script for your app using 'scripts' in setup.py, or let setuptools generate it using 'entry_points'.
Take a look at https://github.com/getsentry/sentry for a good example. After doing 'pip install sentry', you can run the included gunicorn-based HTTP server via bin/sentry ('sentry init && sentry start'). A uWSGI-based server would have worked, too.
I like to create a virtualenv under /opt, install the package and its dependencies with pip, and then run fpm to create an RPM or DEB. Then I use Chef or Puppet to install the package, deploy config
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files, deploy a service script (for upstart or daemontools), and enable the service.
See also http://www.12factor.net/ for some principles on how to structure your app. These can be applied whether or not you use setuptools. For example, Heroku's Python buildpack will deploy your 12-factor app in-place using requirements.txt and Procfile in your app root, ignoring setup.py. I find 12-factor apps are easier to deploy whatever method you choose, since configs/services/logs are cleanly separated from your app itself.