WordPress plugin dev w/ JS library dependencies? Best long term approach w/ source management?

Solution:

To my knowledge WordPress has no real standard for managing JavaScript and CSS dependencies outside of the enqueuing them in the right order.

Using Bower for managing the dependencies is definitely a good idea. It will keep your repo clean of vendor files and make it easy to update libraries later on.

If you want to make your life a little bit easier, you can also look into Grunt JS or Gulp JS which are build tools. You can use these to compress, uglify, etc all your JavaScript and CSS files into distributable items (e.g. all.min.js & all.min.css). This will make it easier to add/remove libraries. Using these will also keep your enqueue statements cleaner.