This article is an eye opener and it has pretty good overall information on how to know whether your system is infected or not. A must read.

http://justanothercoverup.com/?p=608

I really doubt you will read the entire article, so here I copy/paste the last paragraph which also happens to be of more practical use to us.

A good resource to check your system is TrendMicro. Besides producing some good software, they also offer a free scan of your system called HouseCall. It’s best to use Internet Explorer when using this program, however, it is an extremely good scan, and if your system won’t connect to this service, then it’s possible you may have a virus. Make sure and click OK to the Active-X control that will appear at the top of your page to allow Windows to download their virus database and controls. No system is perfect, but as far as free scanners go, TrendMicro is a product you won’t regret using, and it also cleans-up some of the most common Malware that’s currently plaguing our systems. Yes, Housecallwill work even if your system is protected by most anti-virus programs – and you may be surprised, if not angered, by the results.