External JS libraries
I think it highly depends on what the script is. There are definitely advantages to using third party scripts rather than including them locally. In most cases, I'll try to use the google Library API (http://code.google.com/apis/libraries/) when possible for things like swfobject, webfont loader, and the like. The advantage here is that clients may already have these libraries cached, giving a performance increase over hosting them locally. For situations where there is not a widely used third party host for scripts, I'll usually add them to sites/all/libraries/$library_name and include them locally, so you can take advantage of Drupal's ability to aggregate and minify JS.