Don't know any particular program that can do that, and in fact, MSN expects the user/password to be unencrypted to use it, so I find it difficult. In MSN, you can simply uncheck the save password checkbox at the login and it will not save it (don't know if it actually deletes what was previously there). Of course you have to type it everytime.
You can try to delete manually too. It should be stored under your profile folder (by default C:\users\<your account>\appdata), under local or roaming and there the folder "windows live". If you delete all those folders, the saves passwords will go away, but will lose all your settings for those programs.
On the other side, being stored under your profile data means that the Windows permissions only allows you and administrator access to those keys. If you don't share your computer, or other users don't use your very same account and don't have admin rights, your data may be well safe from others.