Since Concrete CMS themes are just collections of PHP template files that correspond with page templates, nothing special is required to use CSS and JavaScript within them. Simply including CSS and JavaScript with directives like this
<script type="text/javascript" src="<?=$view->getThemePath()?>/js/library.js"></script>
will work, and will work well.
You can also use some helper methods here.
<?php
$html = Core::make('helper/html');
print $html->css('path/to/my.css');
print $html->javascript('path/to/library.js');
$pkg = Package::getByHandle('my_package');
print $html->javascript('path/to/library', $pkg);
?>
Including LESS
As mentioned elsewhere, you can also include and parse LESS files by using the getStylesheet method found in in the \Concrete\Core\View\View class.
print $html->css($view->getStyleSheet('main.less'));
This will load a LESS file found in your theme's "css/" directory, write it out to a file found in application/files/cache/css/, and include that file in a CSS tag.