I know how annoying Windows messenger can be; popping up, taking up a space on your quicklaunch bar, and making waste of useful memory to stay running. If you want to disable it completely so that it does not start when Windows does, just follow the steps as follows:

1) Go to “Start–>Run” and when the prompt comes up type “regedit” and hit enter.
2) When the window opens, navigate to HKEY_LOCAL_MACHINESoftwarePoliciesMicrosoft.
3) Create a new key. To do this, go to “Edit” then select “New” then “Key”
4) Name this new key “Messenger”
5) Select this newly created key and create another key called “Client”
6) Now we need to add what is called a “DWORD Value”. To do this, right click on the “Client” key you just made and go to “New” then “DWORD”.
7) Name the new DWORD “PreventRun” then hit enter.
Now all you need to do is give it a data value of 1 (Double click on it then enter 1 in the box).
9) Restart Windows and you will find that Windows messenger has been disabled.