The most common problem I run into now is spyware,
otherwise known as malware. Viruses are still a major concern and while most do not damage your windows installation, they do allow it to be controlled by the author of the virus. They are almost all Trojan Horse types of viruses and there are 1000's of them in the wild.
Below are links to some of the free AV programs, which do a decent job of protecting your computer. If you are in a "high risk" catagory, i.e. downloading software then you might consider Norton or Kaspersky.