When I looked at information about virus scanners at sites like AV-Comparatives, I came to the conclusion that Kaspersky Anti-Virus is best. The scanner part (without realtime protection) is available for free at http://www.kaspersky.com/virusscanner. The interface seems to be a Java applet, but the scanning part seems to use a downloaded executable and downloaded Kaspersky extended signatures.
In Firefox 3.0.3 it couldn't detect Java (even though it Java is installed and functional), but it woked fine in Internet Explorer 7.0. That's fine for me because in Vista the browser must be run as Administrator, and I don't want to run the browser I use for web browsing (Firefox) as Administrator. It allows scanning of critical areas, the whole system or particular folders, and it seems reasonably fast.
Signature based detection of malware isn't a perfect solution, but this is the best scanner. I feel it's definitely good enough for occasional checkups. Note that if you have a file which you actually think might be suspicious, you're better off using one of the web sites which scan it using multiple scanners, like VirusTotal or Jotti's malware scan, and even those aren't guaranteed to catch everything.