There are numerous good free tools for this.  Unfortunately you will need to get to the web to access them.  If your box will not let you get to the web youcan download from another box and then burn the exe files to a cd.  Then copy them to your box's desktop and run from there.

spybot
spywareblaster
adaware by Lavasoft
ccleaner to clean your machine's history etc.

Good luck.

you will need more than one -as they tend to focus on different types of bugs...   trojans, worms, viruses...etc....  there was an article a month or so back in one of the computer rags...  look for similar articles...

I use a combo of XoftSpy (from ParentoLogic) AdAware from LavaSoft, and a package from Norton Internet Security...  these offer free trial packages...  and can be somewhat difficult to use, but worth the effort.

First, make sure your regular operating system is up to speed and is current. Also hopefully, keep all disks of secondary software you have installed since the purchase of the machine. In the immortal words Ripley in the Aliens sequel, "Let's nuke the planet from low orbit.  Its the only way to be sure."

If you can't boot up, re-install.  Don't try for a point in time recovery because that might be corrupted as well.  After re-installation, download SpyBot Search and Destroy, Adware SE. Run those, they are free.  I would then suggest buying McAfee Security Suite and Xsoft's XsoftSpy.  I run all of this stuff and still soemthing will sneek across.  Also, not saying that you do, but watch what porn sites you go to.  Notorious for having shit.

Good luck.

Since you posted this, I am assuming that you were still able to access the internet and your computer still is working. Going from that assumption, it sounds like it was a pop-up ad for a spyware eliminator. How they operate is that you get the ad saying you have spyware, you click on the ad, it "checks" your computer, tells you what spyware you have, and it will eliminate if for a fee. As others have suggested, use Ad-Aware, Spybot Search and Destroy, and Spyware Blaster. The first 2 get rid of spyware on your computer, the third stops it from loading. You also should be using an anti-virus program and have a firewall running. My $.02, for what its worth

IE by itself doesn't tell you that you have spyware, that was an ad...but chances are pretty good that you do have spyware, viruses, and other malware on your computer, so you might as well do a few things just in case.

First you'll want a couple good spyware tools,
I suggest, like others here have, Ad-Aware and SpyBot S&D
Which you can get here:
http://www.majorgeeks.com/Ad-Aware_SE_Personal_d506.html
http://www.majorgeeks.com/SpyBot-Search_&_Destroy_d2471.html

After you install and check for updates on both,
you will want to run themwhile booted into "Safe-Mode" to be most effective.
To boot into "safe-mode":
Restart your computer
before it does anything start tapping "F8"
this will bring you to "boot options" screen
on that screen choose "safe-mode" and hit "enter"
You will want to log into the "Admin" account.
This will load only essential apps. This should keep most of any malware on your computer from running, running apps can't be deleted so easier to remove the malware when it hasn't loaded.
SpyBot S&D might offer to run at boot if it detects something that has loaded if it offers, let it.

Then, I would suggest is that you go to:
http://www.pandasoftware.com/activescan/com/activescan_principal.htm

and run the free online scanner (it will ask to install spftware...let it...I assure you it's safe.    
When you run the scan check the box for "heuristicscan", and have it scan your computer.

Now something you can do to prevent some of this stuff from getting you in the first place is a customized HOSTS file.
You can get a good one here:
http://www.mvps.org/winhelp2002/hosts.zip
and if you ever want to turn it off you can also grab renhosts:
http://www.mvps.org/winhelp2002/RenHosts.bat
that will change the name of your HOSTS file so you can go to sites it has blocked if you absolutlely have to.

To replace the HOSTS file you have go to:
C:\WINDOWS\SYSTEM32\DRIVERS\ETC
in your computer and after "unzipping"  the file that down laoded just drag it to that folder it will ask if you want to replace the file, choose "yes".

Spybot S&D also has an option of using their hosts file as well,
Tools tab
Hosts file
Click "Add Spybot-S&D hosts list"

After doing both these changes to the HOSTS file,
navigate back to
C:\WINDOWS\SYSTEM32\DRIVERS\ETC
right click the file and select read only.
This will keep malware from changing your hosts file to keep you from going to sites for spyware removal and anti-viruses etc.

I should probably tell you what a hosts file is since I am suggesting you change yours. *grin*

Basically all a HOSTS file is, is a list of host names, host manes being the url you type into your browser to go to sites, that is then converted to the IP address of that the site.
Your computer has it's own host, called "localhost" with an ip address of 127.0.0.1
when you add malicious sites to your hosts file it associates that site's Host name with the localhost IP...so when you try and go to those sites, or those sites try and connect to you instead of looking up and going to the sites IP address it just goes to the localhost and you get a 404 for that site, keeping it from coneecting to you...and if it can't connect it can't put anything bad on your 'puter.  *grin*

Now, once any malware has been removed from your computer you will want to be sure your registry is clean so if you are running WindowsXP a great free registry cleaner is RegScrbXP, you can get that here:
http://www.majorgeeks.com/Lexun_RegScrubXP_d2048.html
it will clean out all kinds of crap from your registry, not just malware stuff. This app will create backups of your registry so you can restore it if anything gets fsked up.


Next, go to either:
http://www.sygate.com/firewall/
http://www.zonelabs.com/store/content/company/products/znalm/freeDownload.jsp
and get one of the firewalls.

Also, you might consider either using Firefox as your browser, from:
http://www.mozilla.org/products/firefox/

or at least turning off ActiveX controls in IE:
Tools
Internet Options
Security tab
Custom Level button
set the options for ActiveX Controls and Plug-ins to "disable"  or "prompt".

Hope this helps.  

Adaware works well. Microsoft has a beta spyware remover you can download off their site.