Teamviewer in notification area only
Sure, you can use alltray for that :)
Look it up in Applications -> Ubuntu Software Center, or use this command:
sudo apt-get install alltray
EDIT To minimize the program, run alltray and point to the Window of it. It will hide in the tray. To hide/unhide to/from Tray, click the Tray icon of the program :)
It's an application-specific behavior - you'd need to get the app makers to change it. However, moving it to another desktop will also cause it not to be an eyesore, while alltray as Karni suggested would fill the tray part.