Menu icons are not loading after restart
This can be caused by missing/corrupt menu items that hook into the SystemUIServer such as first-party menu items or apps like iStat Menus which integrate into the SystemUIServer (you can usually distinguish these because you can ⌘-drag them between other apps' menu bar items.


Check the log in Console.app (/Applications/Utilities/), looking for any apps which you know have menu bar items present, or any references to SystemUIServer.
Check Activity Monitor for any apps that show Not Responding for their process.
Try restarting SystemUIServer and watching to see if you can notice the hanging app:

killall -HUP SystemUIServer

You can use the Accessibility Inspector, accessible from Xcode → Open Developer Tool → Accessibility Inspector.

Hover over the item and the pane may show you enough information for you to determine what it is. For example, hovering the Dropbox menu bar item shows "Dropbox &lt;version>" under AXHelp, and hovering Little Snitch shows "Little Snitch Agent" under AXTitle.