sharepoint2010 : javascript in Sharepoint 2010 using visual studio 2010-Collection of common programming errors

You can utilize JavaScript in your web parts just as you would HTML or CSS. As for it’s location, a common place to store these files is in the Style Library. You would then create a reference to the JavaScript file in your masterpage or page layout (depending on your needs) where it would be available at runtime.

I would recommend using SharePoint Designer for managing and versioning these style-related files.