IMO I will have separate tags for separate javascript snippets/plugins, it will make my javascript code easier to maintain. I can remove the plugin/add the plugin without disturbing the other javascript snippets.
But for performance issue, modern browsers will run 6 consecutive threads to download the resources, so it will be good idea to profile the loading times of the site/web app. You can use tools like Firebug/yslow to profile http requests being sent from the html page.
Personally I use template engines like Sitemesh and create templates for jsps for different parts of the application.
And for javascript I mainly use JQuery and a lot of plugins.