Per Yahoo it's best to move your Javascript calls to right above your closing body tags since downloading scripts block parallel downloads which causes your page to take longer to download/render. (1) Now I'm not going to go into any metrics to prove this statement, we'll just have to take Yahoo's word on it.

At the last Florida Drupal meeting one of the attendees (sorry, I'm horrible with names) asked why Drupal was so difficult to upgrade.  At first we were a bit confused since we thought Drupal was easy to upgrade but we later found out that the user was storing his modules in /modules and themes in /themes so every time he wiped out his Drupal installation he had to re-install all of the files for his modules/themes.  While it sounds like this is uncommon, I can assure you, it's quite common for new (and some experienced) users to make this mistake.