I would first use Disk Utility in your Utility folder to Repair Permissions. If that doesn't help, do the following.
For Safari, look in here and see if Bookmarks.plist is there;
User>Library>Safari
For Explorer, look here for Favorites.html
User>Library>preferences>Explorer
If those files are there, I would drag them to the desktop, restart, then put them back and see if they show up.
If not there, do a Find for them and see if they turn up.