My little experience with the queue of scripts

• Sometimes you might be surprised, that WordPress/even­tually a plugin (from an unknown reason) enqueued jQuery (not speaking about administration but public template!). De-queuing is simple: Call wp_deregister_script('jquery'); before wp_head(); is run, where the scripts are usually printed out from the queue. 
• I think it's good time to stop inserting <script> tags into templates directly. As I found out, the queuing principle is quite useful. Especially thanks to the
  1. dependency principle: that will care about all that cases, where the order of scripts' including is important (jQuery first, Thickbox only after)
  2. the version check: causes that the newest queued script is included (let's say one plugin enqueues jQuery 1.3 and other 1.2.1 – the newer will be used automatically). well, it's just to be sure the the updated script will be downloaded to client, and won't be used the cached version.
• loading own modification of script and not the version distributed with WP

wp_deregister_script('thickbox'); // unload the possible attempts of loading default thickbox
wp_enqueue_script('thickbox_my', get_bloginfo('template_url') . '/scripts/tb.js', 'jquery', '3.1' ); // just can't load own thickbox and use the 'thickbox' handle

But I'm still not sure this method of inclusion is so much useful in case of style sheets. Here I will stay by static <link> insertion, for now.

See also: Codex/Function Reference/wp_en­queue_script

Update: sorry about the mystification with „auto-choosing the newer version“. I don't know why I believed that WP behaves so.