The best way that I've found to keep from getting pop-ups like crazy... is to back up anything you want to keep on your computer (things that can't be re-installed, ie: photos, some documents... things like that) and format your entire drive... then, when re-installing windows, partition the drive into two parts, the first partition, C:\ around 10 gigabytes, and the second partition with the rest of the space... keep only your Windows installation and other system installations (like AIM or Yahoo Messenger) on the C drive as well... then keep whatever else you want (games, photos, music, etc.) on the other drive... whenever your computer becomes too cluttered, you can re-format the C drive and keep the other drive full of things... it only takes about a half hour to format the C drive and GUARANTEES that you get rid of all of the spyware crap... it'll make your computer run like it did when you first bought it ^_^
Secondly, don't go to websites that are shady enough to have spyware downloads on the sites (ahem, like pr0n sites)... you really only get those things from sites like that anyway... you could get a pop-up blocking browser, also... I recommend Avant Browser (or FireFox... lots of people swear by it... but I like my Avant more ^_^)
It might sound kind of difficult to format and all that... but if you find somebody who knows what they're doing (preferably a friend... and not an overcharging computer store) it's not too difficult...
By keeping my drives separated and able to be re-formatted, using pop-up blocking browsers, and not going to shady pr0n sites... you can basically eliminate spyware on your computer ^_^
*NOTE* This won't work if you have a Dell/HP/Compaq etc. store-bought computer... they partition the drives themselves and make it a hassle to do it this way...
Oh, and you haven't suffered "a virus attack" that's just silly ^_^
It's what myself and all of my computer geek friends do... it just makes sense... I've used Spybot Search and Destroy... Ad-Aware... Webroot SpySweeper... all that stuff... and they don't always work... ::shrug::