hook_form_alter() doesn't take $form_state as a reference

Fixed in dev.

Actually it does. According to the documentation it's not supposed to - but if you follow the code you'll see that it does pass it by reference. (I'm using D6-13).

Just use ..._form_alter(&$form, &$form_state, $form_id), and you can add stuff to $form_state.

Which was very handy for me because I had a multi-page sub-form to insert into various other forms on the site. The sub-form could have been half-completed in one place then reappear in the same state somewhere else - I needed to be able to set up $form_state['storage'] with the correct starting conditions. Which would have been impossible without this.

The documentation is being fixed on that to show that it is indeed passed by reference.