What can I hook into after_setup_theme?

Think of WordPress execution as a series of rungs on a ladder: WordPress climbs one rung, then the next, then the next, and so on.

Think of action hooks as the rungs themselves. Here is a (slightly abbreviated, I think) list of those actions, or “rungs” executed during a typical WordPress request.

Thus, an add_action() call is simply an instruction to execute a function on a specific rung on the ladder. As long as you make that add_action() call on a rung earlier than the run on which you want the specified function to execute, then it doesn’t matter, per se which rung you use to make the add_action() call. However, there are reasons to use specific rungs to execute functions.

To take your example: a Theme’s functions.php file executes at (I believe) after_setup_theme. So, you simply can’t use a Theme to add an action to any rung prior to after_setup_theme, because WordPress has already executed those actions (i.e. WordPress has already climbed those “rungs” on the ladder).

If you try to execute wp_enqueue_script() in a callback hooked into an action before init, WordPress will generate a _doing_it_wrong() notice, because wp_enqueue_script() should not be executed before init, and most correctly should be executed at either wp_enqueue_scripts (front end) or admin_enqueue_scripts-{hook} (admin).

However:

Can I chuck stuff like this in there too?

add_action('get_header', 'enable_threaded_comments');
add_action('widgets_init', 'unregister_default_wp_widgets', 1);
remove_action('wp_head', 'rsd_link');

All of these are perfectly fine being called at after_setup_theme, since all of the specified actions fire later than after_setup_theme. With add_action(), you’re simply telling WordPress, “queue up this callback at the specified action.” With remove_action(), you’re simply telling WordPress, “remove this callback from the specified action.”

Edit

In re:

Great answer – thanks. I understand most of it, but a little confused why all my calls to hooks with the add_action and remove_action are ok but the call to wp_enqueue_scripts isn’t? They all fire after after_setup_theme. I know you said it’s because I can’t execute wp_enqueue_scripts before init; though without you telling me that how would I know? For example, how do I know if there is anything else that can’t be executed before something else.

Because add_action() simply queues up a callback, inside of which functions are actually executed. But functions like wp_enqueue_script() or wp_enqueue_style() are actually functions, that execute wherever you call them.