I've being getting a lot of popup ads when I've being using MSN Messenger. Final sorted it out so if your having the same problem this is what you do, oh this is for XP by the way.
Right click on 'My Computer' icon on the desktop and select 'Manage'. In the 'Computer Management' window, click on the “+” sign to the left of 'Services And Applications'. In the tree that opens up, click on 'Services' scroll down the Services menu, locate 'Messenger', right click and select 'Properties'. In 'Startup Type', choose 'Disabled' in 'Service Status', click on 'Stop' Then click on 'Apply' then on 'OK' to close, then close the 'Computer Management' window.