Being the computer geek, I think I should explain this... +rep me if you feel that this is helpful.
Pop-ups and Pop-under ads are just a way that advertisers get to you. They are normally "javascript"ed. They basically just spawn a window into some predefined location of your screen. They are very very annoying. Pop-up blockers may help, but every once in a while, a new method is created to evade the recognition of it as a pop-up (after all, the blocker won't block it if it doesn't think it is a pop-up in the first place).
The first step into removing pop-ups is by removing all spyware and adware from your computer. Use
http://www.lavasoft.com"] Ad-Aware Personal [/URL] to remove the most recognizable spyware and adware. Then, pay for a commercial spyware remover to completely clear out your computer.
Usually, if you downloaded P2P softwares such as BearShare and KaZaA, you will receive a bunch of spyware in the free version. Almost any game, software, or whatever that is free is powered by ads. Or else, where would they get the money to make it in the first place?
If you removed every P2P software or anything suspicious and still receive pop-ups, then they must be spyware. Spyware is a more malicious version of AdWare. Unlike Adware, which can be convieniently removed, spyware is there to monitor your activities and send them to a database and keep on flashing pop-ups. Get Spyware Doctor to clear them all out.
Yea, that's basically it.