Hey @MattOnce,
This javascript plugin is fairly easy to setup and has great documentation. Fancybox | Fancyapps
Besides videos in popups you can create gallerys, lightbox, etc. as well
It should be pretty easy to setup, my colleague recently wrote a blog post on building a custom module. Building Your First HubL Custom Module [Free Module] The module mentioned in the blog actually uses the plugin above.
IF you have any questions on setting it up please feel free to shoot me a message