The $menu variable in the themes header.html does too many things.
On the front page of your Moodle it tells you who you are logged in as as well as allowing you to choose a language (as long as that option is switched on)
On Course index pages it only tells you if you are logged in.
On Resource pages it gives you a button for viewing logs (again, only if switched on), a jump menu, and a previous and next button.
All of these things are pretty cool, but it's a bit of straightjacket that you can only specify them to be in one place and, by extension surround them with a single bit of HTML and CSS style.
You may well want all of the above to appear but in different places and styled differently. Or you may only want some elements e.g. the jump menu without the backwards and forwards arrows.