Welcome to the site.
As for pop ups, you don't say when you are getting them, but I do have some general advice.
First, you need to check for Spyware (programs that are frequently downloaded by websites taking advantage of security problems in IE).
I personally use Adaware (
http://www.lavasoft.com/software/adaware/), spybot (
http://www.safer-networking.org/en/index.html) to clean my system.
I use Spywareguard (
http://www.javacoolsoftware.com/) and (at the moment) Microsoft AntiSpyware beta (
http://www.microsoft.com/athome/secu...e/default.mspx), although that is beta software (so may not work) and Microsoft are considering charging for it. You should also be aware that the microsoft.com website will check you have a legit copy of windows before allowing you to download it (not sure if you can bypass this)
Spywareguard, Microsoft AntiSpyware and Spybot work well together to prevent any spyware even being installed.
Next, having run all those, make sure you have a good firewall installed. I personally recommend ZoneAlarm (
http://www.zonelabs.com/store/conten...ku_list_za.jsp). It should block the relevant ports to stop Windows Messenger boxes appearing (the ones that appear in the middle of the screen, with an OK button at the bottom).
Finally, I would recommend using Windows Update to check you have all the latest critical patches and service packs installed.
I am assuming you are using a PC and a version of Windows. All the software I have mentioned is free, although with some (Adaware, ZoneAlarm and Spywareguard) you do get some nice extras when you pay for them.
Finally, as stated above, if possible, use an alternate browser (Firefox, or my favourite, Opera). It's a good idea to all the stuff in this post anyway.