Anti-Virus

One thing that plagues Windows machines, and is a source of much frustration for users, is its susceptability to viruses. There are now approximately 114,000 known viruses which can infect Windows.
There is a malware/virus database maintained at Viruspool.net, which as of this writing contains 784,654 virus descriptions of 45,159 unique samples. There's also the WildList Organization, which maintains lists of actively circulating viruses.
It is commonly argued that there are so many viruses which affect Windows because it is so popular or common and that if MAC or Linux was in use on as many desktops as Windows is, viruses would still be just as much of a problem. This is simply not the case, for more on this particular point see Security Report: Windows vs Linux. The design of Windows is inherently insecure compared to the other two main operating systems (MAC and Linux/*nix). One might say that this is a side effect of it's user-friendliness, given that the user is allowed relatively unrestricted access to the system kernel and related files thus giving any program that is run the ability to make system changes at-will. The Operating System started as a standalone single-user workstation OS and even with the changes of incorporating the NT kernel into 2000 and the multi-user design of XP, it hasn't shaken the insecurities in architecture it was born of. This is not to say that Linux or MAC machines can't be compromised, but their design simply makes it more difficult to do so. See the Security page for more details.
There are reportedly 863 known viruses for Linux as of 2006. Of these 863, only a handful are known to exist in the wild. The overwhelming majority are "proof of concept" or lab viruses. As mentioned here, it is difficult for a virus to infect a Linux system.
Running Windows viruses with Wine An amusing article from which the following is quoted: "Out of the five Windows viruses I ran under Wine, not a single one was able to send email and propagate itself. When I went out of my way to be part of the Windows community by doing my part to propagate Windows viruses (lots of Windows users seem to think this is important, seeing as how they run random executables and use Microsoft Outlook and Internet Explorer) I discovered that it couldn't easily be done with GNU/Linux tools. Oh sure, I could manually forward these viruses to the folks in my address book, but where's the fun in that?"

Of course the best Anti-virus is to use an Operating System that is relatively immune to viruses to begin with. While Mac and BSD variants also fall into this category, Linux is our general recommendation. See the Linux page for more info and suggested distributions.
Top 10 Ways to Protect Your Linux Home System
A machine which has been infected should be formatted and a clean install should be performed, unless there is well documented details on the particular infection and it can reliably be cleaned without reinstalling. Regardless, the only way to be sure that the machine is no longer compromised is to reinstall, and the only exception here would be someone whom has vast knowledge of malware, security, and forensics that can verify the system is no longer compromised.
Why do I have to format and reinstall Windows after my computer is infected with a virus? from the Indiana University IT knowledgebase.
When should I re-format? How should I reinstall? from the DSLreports.com FAQ
IT Security: System Compromise FAQ from MIT's IST dept.

• AVG Anti-virus from Grisoft
• Kaspersky
• WinPooch - "Winpooch is a Windows watchdog, free and open source. Anti spyware and anti trojan, it gives a full protection against local or external attacks by scanning the activity of programs in real time. Associated with ClamWin antivirus, Winpooch keeps safe your computer against virus."

Additional Info

Independent comparisons of some AV programs can be reviewed at av-comparitives.org.
Developers interested in Anti-Virus programming may be interested in the Open AntiVirus project.