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I am using Elementary OS Freya and since I installed a program not using the included software manager, I get an icon in the menu bar like this: 
I tried to do
sudo apt-get update -> Sudo apt-get upgrade
Then I installed the packages that were held back and did
Sudo autoremove
I am a noob at this sorry..I noticed that Unity was installed too..
This question has been asked before and already has an answer. If those answers do not fully address your question, please ask a new question.
Open task manger immediately after you login to your computer and check which application is running and does not show its icon. For instance, Dropbox does that. To make sure which application missing just try to treminate that application this will remove the icon from the topbar.
Your icon-theme have'nt the application icon, look in internet the icon that's you like an put it in the folder of your icon-theme as root. Logout. Excuse my english.
