By default, Microsoft includes a Links folder in the Favorites menu of Internet Explorer. Many users never use this folder, choosing instead to keep their bookmarks in folders with more specific names. Here is how to hide the Links folder from the list.
Using Explorer, find the location of your Favorites folder (e.g., C:\Documents and Settings\username\Favorites).
Select the Links folder. Then right-click and select Properties. Check the Hidden checkbox, and click OK.
Now, open up IE, and go to Favorites. Delete the Links folder from the menu.
From now on, the Links folder should be hidden from the Favorites list.