Runscanner isn't a tool for everybody. It's not as easy to use as other, more well-known, free anti-spyware tools such as Ad-Aware--and doesn't appear to peer as deeply into your system as they do. It won't, for example, report on cookies that might be invading your privacy.
Rather, it's more like HijackThis, which is designed more to find home page hijackers and similar threats than garden variety spyware. Run Runscanner, and it does a quick scan of your system for more than 100 hijack locations and similar potential problems. Depending on whether you run it in Expert or Beginner mode, it then shows you the results and has a tool for killing the potential infection (advanced mode), or else creates log files that you can upload to forums where people will analyze your logs and let you know if you might have any problems.
Because of that, this tool is best suited for when you think you might have an infection, and no other spyware killer or anti-virus can detect it, in the same way that HijackThis is used. However, because HijackThis has a larger user base, there may be more experts familiar with it than with Runscanner, so HijackThis might be a better bet for protection.
Note: This program is donationware. It is free to try, but the author accepts and encourages donations towards further development.