front page - whether blog posts index or a static page front-page.php Front Page setting (settings -> reading) Home Page (blog index) setting (settings -> reading) Ideally, if you have a front-page & blog page, you will use Reading Settings to assign the blog page to put WordPress in control over the loop. Front-page
A scripts that add functionality that the site needs custom post types custom metaboxes tracking scripts removing elements to be gone regardless of theme
A moving a menu removing elements for a specific look/layout filtering the byline custom footer function enqueueing theme-specific fonts or styles or scripts registering sidebars