I have been using Grisoft's Free Antivirus and Spyware software with good success and they have put out a rootkit for detecting malware that hides in the system and is hard to detect.You can find all of them
Here
It also might be a good idea to check your firewall settings. I have seen a few times where trojans have a wonderful time turning off your firewall and then you have IE messenger pop ups. They look like IE windows but are actually random IE messages that are sent randomly to IP's in hopes of opening a window.
