As other people have said, when you put javascript in the head it delays the rendering of the page until after the scripts have loaded, which means the page may take longer to load - especially if you are downloading large script files.
If you move your script tags to the end of the page, you will ensure that the browser downloads images and stylesheets before the script tags and the page will likely apear to be rendered before the scripts start to run. This also means that if you are depending on some functionality from your scripts, this will not be available until a bit after the page is visible to the user.
If you are adding styles or elements (etc. switching textfields with some form of richer editor) this will be visible to the user as flickering.
If you are adding click-events to elements, they will not be clickable until a bit after the elements themselves are visible.
Sometimes theses issues requires you to put your scripts in the head, other times you will be fine by sticking them in the bottom.
IMHO (completely against YSlow and lot's of clever people) you should keep your scripts in the head tag, and just rely on them to be cached most of the time.