If you still want to use IE:
Goto c:\windows\downloaded program files\
and Delete all the plugins except that of Java, Shockwave and Quick Time.
visit
www.doxdesk.com // identifies most of the spywares
Install and run Spybot & Adware
Install Google toolbar. pretty cool in stopping popups.
If you are running Windows XP, stop the Messenger service. To do Right clikc My Computer Icon in the Desktop and choose Manage.
Choose Services, and scroll down for Messenger service. Right click and choose Properties. In the properties dialog choose the Startup type as Disabled. You dont need this service, because this is only used to send and receive messages in a network. MSN messenger will have no problem when this is disabled.
Also try Autoruns.exe from
www.sysinternals.com, to check what all programs are started during ur system startup.