IMPORTANT
If you are using ME or XP and you are trying to get rid of an infection DISABLE SYSTEM RESTORE FIRST, or if you ever do a restore you will restore an infected system and the infection will come back.
McAfee's page on disabling system restore:
http://vil.nai.com/vil/SystemHelpDocs/DisableSysRestore.htm

FREE online scans

(Note most online scans require I.E.5.0 or more recent - you can't use other browsers)

http://www.pandasoftware.com/activescan/com/activescan_principal.htm
OR alternative location http://www.pcpitstop.com/antivirus/

http://www.pcflank.com/trojans_test1.htm (quick anti trojan test)

http://www.trojanscan.com/ This is the A2 scan (for program to delete trojans see below)

http://housecall.trendmicro.com/
OR http://housecall.trendmicro.com/housecall/start_corp.asp

http://www.bitdefender.com/scan/license.php

http://us.mcafee.com/root/mfs/default.asp?cid=7466&affid=
OR alternative location: http://www.pcpitstop.com/freescan/
OR http://us.mcafee.com/MySecurityStatus/default.asp?cid=9915
(I'm not sure how this differs from the McAfee scan immediately above)

http://www3.ca.com/securityadvisor/virusinfo/scan.aspx

http://www.pestpatrol.com/prescan.htm?cj=pestscan (Spyware scan)
OR alternative location: http://pcpitstop.com/tinylink.asp?pestpatrol

http://www.digitalriver.com/v2.0-img/operations/safer/site/ab/promo53026.htm

http://download.zonelabs.com/bin/promotions/spywaredetector/index4.html

http://www.spywareguide.com/txt_onlinescan.html

FREE Anti virus programs - Scan with as many as you can, but only have one sheild running permanently

AVG http://www.grisoft.com/doc/289/lng/ww/tpl/tpl01

AntiVir (Now much faster to update definitions than previously)
http://www.free-av.com/

AVAST (Note when I sent them a trojan they missed they hadn't add it to their list days later)
http://www.avast.com/eng/avast_4_home.html

CLAMWIN (Note this scan is VERY slow and when I sent them a trojan they missed they hadn't add it to their list days later)
http://www.clamwin.net/

F-PROT (Scan only - no sheild) Download and unzip this dos antivirus program from here: ftp://ftp.complex.is/pub/dos/
Download and upzip the definition files (macrdef2.zip and fp-def.zip) from here: ftp://ftp.complex.is/pub/
Unzip them into the same folder you unzipped the program into.

FREE Anti virus and trojan cleaners

http://www.avast.com/eng/down_cleaner.html

http://vil.nai.com/vil/stinger

http://www.trendmicro.com/download/dcs.asp
For this one download sysclean package into an empty folder then download the virus defintions into the same folder
These are found at http://www.trendmicro.com/download/pattern.asp

FREE Anti spyware programs - Scan with as many as you can, but you might wish to only have one running permanently to avoid slowing down your computer

AdAware http://www.lavasoftusa.com/software/adaware/
OR http://www.pcworld.com/downloads/file_download.asp?fid=7423&fileidx=1

Spybot search and destroy http://www.safer-networking.org/en/index.html
OR http://www.pcworld.com/downloads/file_description/0,fid,22262,00.asp

Microsoft Antispyware (for XP only - free at the moment) I only don't recommend this as I can't test it, I don't use XP)
http://www.pcworld.com/downloads/file_description/0,fid,24761,00.asp

Other useful FREE Anti spyware programs/tools

Spybot reccomend that you also install SpywareBlaster
SpywareBlaster http://www.javacoolsoftware.com/spywareblaster.html

Spyware Guard http://www.javacoolsoftware.com/spywareguard.html

CW shredder http://www.pcworld.com/downloads/file_description/0,fid,23551,00.asp

Silencer (this stops spyware program communicating it doesn't get rid of them) http://www.pcworld.com/downloads/file_description/0,fid,22889,00.asp

Yahoo toolbar with AntiSpy http://www.pcworld.com/downloads/file_description/0,fid,24025,00.asp

Hijack this http://www.pcworld.com/downloads/file_description/0,fid,23258,00.asp

Spyware Blocklist file http://www.pcworld.com/downloads/file_description/0,fid,23740,00.asp

IE Spy-ad http://www.pcworld.com/downloads/file_description/0,fid,23332,00.asp

FREE Anti malware programs (trojans, spyware, viruses etc)

Ewido (for XP only) I only don't recommend this as I can't test it, I don't use XP)
http://www.ewido.net/en/

A2 http://www.emsisoft.com/en/software/download/

PrevX (for XP only) I only don't recommend this as I can't test it, I don't use XP)
http://www.prevx.com/prevxhome.asp

XCleaner http://www.xblock.com//download-freeware.php

FREE Firewalls - you can only use ONE of these

http://www.kerio.com/kpf_home.html

http://www.zonelabs.com/store/content/company/products/znalm/freeDownload.jsp

http://smb.sygate.com/products/spf/summary_spf.htm

Keep windows patches up to date here:
http://windowsupdate.microsoft.com/ (You must use Internet Explorer to do this)

Useful programs for getting back control of your computer

Winpatrol allows you to see running processes, startup files and stop them or disable or kill them http://www.winpatrol.com/winpatrol.html

Useful program to find out what is running http://www.sysinternals.com/Utilities/ProcessExplorer.html

If you know which program it is you can delete it in dos or use http://www.softwarepatch.com/software/moveonboot.html

Registry Cleaners (2 different programs with the same name)

RegCleaner: http://www.tweaknow.com/RegCleaner.html

Regcleaner: http://www.majorgeeks.com/download460.html