A great deal of popups are part of the fuctionality installed when using free programs or browser toolbars on the WIndows platform.
The biggest issue with WIndows is it runs all applications with administrive privileges as such they can do what they want to the system
Windows also does not display everything which is running on your system at start up which is where most of these applications which present popups hide and load.
The first thing you need to do is detemine what your computer is loading at startup. To do this download an application called hijack this from Trend Micro
http://free.antivirus.com/hijackthis/
HijackThis examines certain key areas of the Registry and Hard Drive and lists their contents. These are areas which are used by both legitimate programmers and hijackers. Some items are perfectly fine. You should not remove them. Never remove everything. Doing that could leave you with missing items needed to run legitimate programs and add-ins.
The following URL provides information on using Hijack this
http://www.whatthetech.com/hijackthis/
The following forums are a great resolurce for the removal of malware which it sounds like you may have
http://forums.whatthetech.com/Are_you_Infected_t106388.html
Alternativly if you want me to review your hijack this log simply post it to the forum and I would be happy to have a look.
Edited: 18/12/2010 at 21:13