Yes, you can but what we do not offer at the time of this writing is the ability for you to load your own custom javascript libraries to your web server. So there are some limitations on how to do this.
There are generally two ways to deploy javascript. When dealing with a relatively small javascript (js), you can simply add the js code directly into the page, sidebar, or homepage item by pasting it via advanced mode. As long as the js is valid code, it will work as expected.
In a case where the js files are substantial, the more common practice would be to load the js files onto the server and call them with a small line of code in the page. If this is the case for you, then the best option would be to load the js files to any 3rd party server. Amazon AWS is a good option, as is Rackspace, and many domain registrars have services like file-hosting available. Once you've acquired a storage place for your js files, load them, and call them in the page, sidebar item, or homepage item, exactly as you would if they lived locally, except you will use the full URL of the js files.
PLEASE NOTE: Adding custom javascript is for expert-level users only. This is not supported by standard product support.