This may seem a little overkill, and some of it maybe. However it will give you a reasonably secure PC. Not only will it get rid of popups/popunders it will help too keep malware like adware, spyware, and viruses off your pc. Personally I use Debian GNU/Linux and don't have to worry about spyware, trojans, adware or viruses.

For detailed security checklists and more information see "Internet Security Overview "

1) Use a Mozilla browser (Mozilla suite, Netscape or Firefox), preferably Firefox. If you must use IE only use it on secure sites like your bank,etc. Never for surfing the net unless you know how to set all the security and privacy features properly.
"Locking down Internet Explorer remains important even if you're not regularly using Internet Explorer to browse the internet. " Spyware Warrior: Getting Help w/ Spyware
"Another way to disable IE"
{C}http://forums.mozillazine.org/viewtopic.php?t=185554{C}

2) The first thing to do is to make sure these pop-ups are not being generated from within. Many parasites, adware enabled software downloads and P2P files will create pop-ups. Remove them by scanning your system for spyware and parasites. See #3.

Next make sure these pop-ups are not "Messenger Service Spam".
GRC: Shoot the Messenger

3) Install good antispyware and run the scans 3 times. Update regularly.
Know "How to Detect Spies"

Before using any removal programs check them out first at:
"Rogue/Suspect Anti-Spyware Products & Web Sites"
"Protecting your PC w/ quality anti-spyware applications"
"What Adware/Spyware can do"
These programs are excellent aids in the removal and prevention of spyware and other nuisances.
Spybot Search and Destroy
Spyblaster
Spyguard
Adaware
Hijackthis
CWShredder V2.13 is the latest defense against the new Cool Web Search variants.

4) Use Firefox's Popupblocker to allow popups only from sites you trust.
5) Do not accept cookies from any site you do not trust. Also check from "originating site only."
6) Clear your Cache frequently.
7) Use a good antivirus program. Why pay for one when there are good free ones?
Use an antivirus that is updated daily and make yourself a schedule for scanning (once a week, once a month,twice a month). When I ran WinME my system was scanned daily at 4am.
If you don't have an anti-virus program, you can scan your computer with one of these online anti-virus scanners"
AVG
AntiVir
F-Prot
Avast
Clamwin


8 ) Use a HOSTS file to block ads, banners, cookies, web bugs, and even most hijackers. This is accomplished by blocking the Server that supplies these little gems. Example - the following entry 127.0.0.1 ad.doubleclick.net blocks all files supplied by that DoubleClick Server to the web page you are viewing. This also prevents the server from tracking your movements. Lock your Host file so it is read only. For more detailed information and a good HOSTS file to use visit;
"Blocking Unwanted Parasites with a Hosts File"

Add a list of ad servers to your hostperm.1 file to block ads.
A list of ad servers and how to use them to easily block 90% of ads on the web
http://pgl.yoyo.org/adservers/serverlis ... hostperm.1

Or you can use Bust Banner Ads with Proxy Auto Configuration

Use a Proxy Program:
Guidescope
Privoxy
Proxomitron
DansGuardian
Squid Web Proxy Cache

DO NOT use one of the anonymous open free proxy lists.
While thinking that you have made yourself more secure, you have actually opened yourself up for attack. When using an open proxy server, your PC is making a direct connection to another computer. You also do not know who is in control of this computer. Your passwords can be sniffed and your firewall tunneled. Your privacy can also be invaded as this person reads your email, snags your ICQ, IRC, AIM, MSN messages or any other unencrypted data.

If you need to be anonymous use one of the paid services. They are legit and safe.
The Proxy Connection
Anonymizer
Proxify
Steganos Internet Anonym

9) Use a good firewall. Read the manuals. Know how to set program permissions. For help configuring
your firewall see "Summary of Can't Connect/timeout Solutions"
Pay attention to what programs are requesting access. If you don't know what it is say deny.
Outpost Firewall
Zonealarm
Kerio Personal Firewall
Sygate Personal Firewall

10) Install the Adblock extension
Install the newest set of filters from Filterset.G @ pierceive.com Check for updates frquently, usually once a week.
Try adding /[\/.]*popup*[\/.]/ To Block popunders as well as popups.

11) Add a Startup Monitor to your Layered Protection. WinPatrol

12) Uncheck Allow Websites to install software. You can make exceptions for the ones you trust.

13) In your Javascript options only click "Change Images".
Get the <b>NoScript extension</b>
NoScript provides extra protection for your Mozilla Firefox browser: this extension allows JavaScript execution only for trusted domains of your choice. This whitelist based pre-emptive script blocking approach prevents exploitation of security vulnerabilities (known and even not known yet!) with no loss of functionality.

14) Flash popups seems to be everywhere on the net. Here is how to take care of them.
If you do not use Flash you can uninstall it or block it by adding the following to your userContent.css
/* Disable Flash */
embed[type="application/x-shockwave-flash"] {display: none !important;}

The Flashblock extension allows you to click and turn it on.
Spyblaster can set a kill switch disabling Flash.

15) You can add the following to your about:config to stop plugins from opening popups.
privacy. popups. disable_from_plugins Integer
Sets limits on popups generated from plugins (e.g. Flash)
0: lets all popups through
1: limits their number to dom.popup_maximum (even with popup blocker disabled)
2: blocks popups from plugins

16) Disable Java and only use it when you really need it. Turn off the Java Cache.

17) Secure your incoming emails. Use Thunderbird and not Outlook.
Use a email Spam filter. Use plain text instead of HTML.
Make sure your Anti-virus program scans your emails.
Windows: "SpamPal is a mail classification program that can help separate your spam from the mail you really want to read." I recommend using the "HTML Modify Plugin" Plugin Guide HTMLModify removes Javascript, Applets, Sounds, Webbugs in html emails, so that you can use your email program for reading HTML-Mails without giving Spammers/Hackers the chance to damage your PC or to track their mails. HTMLModify will also rename dangerous file attachments that could contain a virus (such as .bat,.scr etc. etc) and may, as a result, stop such a file form auto-running.

Linux: SpamAssassin: uses a wide variety of local and network tests to identify spam signatures."

18 ) Don't use ActiveX and block bad scripts. (Firefox does not use ActiveX unless you have installed the extension/plugin)
AnalogX Script Defender
SpywareBlaster systematically sets the kill bit for a long list of known ActiveX spyware.

19 ) Install a anti-trojan program. Anti-Trojan Software Reviews

20) Empty the Recycle Bin frequently.

21 ) Download and run CCleaner as the Temp folders should be cleaned out periodically as installation programs and hijack programs leave a lot of junk there.

22) Defrag the hard drive regularly especially after CCleaner.

23) Download Windows Prefetch Clean and Control if you use WinXP then run it and clean the Prefetch monthly. There debate whether this is actually helpful or whether it hurts your system Use with care.

24) Keep your OS updated with the latest patches/service packs.

25) Be careful when installng programs. Never download anything if it is not from trustworthy site.
"Staying parasite-free"

26) By all means, be extremly careful when using any P2P file-sharing programs. As they can be spawning vats for viruses. Cracked and pirated programs are especially dangerous.

27) Practice safe surfing. "Safe Surfing"

28) Here is a good site to help one understand pc security and to take preventative measures.
Privacy and Security

By taking most of the above steps not only will you keep your system free of malware but also help others stay free by stopping the spread of malware. Be Safe not sorry.
<b>If all you are worried about is blocking Popups follow the first post.</b>