You may miss the tray icon for Windows Live Messenger on machines running Windows Server 2008, Windows Server 2008 R2 or Windows 7. The process is running, you get – depending on configuration – bubble notifications, but see no tray icon to open messenger window.
Refer to article
http://www.sevenforums.com/tutorials/3794-windows-live-messenger-taskbar-notification-icon.html,
set the compatibility for msnmsgr.exe to Vista (on Windows Server 2008 R2 or Windows 7) or Windows XP (for Windows Server 2008), restart Messenger (just kill the process and restart) and enjoy!