How do I add JavaScript to a site?
The Managing JavaScript in Drupal 7 guide provides the information to add JavaScript to Drupal. The techniques presented there apply to both themes and (custom) modules:


Add a scripts[] = somescript.js to your module or theme's .info
file
Use drupal_add_js() in your module or theme's code
Use the #attached['js'] property in a Form API or renderable array.


Note that Drupal already include jQuery, jQuery UI and a bunch of other libraries so you don't, and shouldn't, add them yourself. Instead you should use drupal_add_library() or the #attached['library'] property.

The Working with CSS guide provides the information to add CSS to Drupal. Again, the techniques presented there apply to both themes and (custom) modules. With an exception: addition of style sheets from an .info files only works for a theme and not a module.


Add stylesheets[all][] = somestylesheet.css to a theme's .info file.
Use drupal_add_css() from module or theme's code.
Use #attached[css] property in a From API or renderable array.