Sometimes you need a second opinion when it comes to the subject malware (i.e.: virus, worms, spyware, etc.). Although, first and foremost you should be running a real-time malware scanner with up-to-date signatures. Then on those occasions where you think something maybe wrong, then you should use an alternate tool to make sure that your current tools are not missing something.
Until recently I have not found an online malware scanner that I like, until I came across Panda's NanoScan. This is a browser based utility, so it requires a plug-in for Firefox and an ActiveX control for Internet Explorer.
This scanner doesn't do a deep scan of your system, it only checks the active processes against a database of known malware. It also doesn't remove any malware, it just alerts to you to their presence.