1. Microsoft Process Explorer (formerly Sysinternals)Process Explorer provides an excellent way to determine what processes are running on a computer. It also describes the function of each process. More important, you can use Process Explorer to create a baseline of the running processes used by the computer when it's operating correctly. If for some reason the computer starts behaving poorly, run Process Explorer again and compare the scans. Any differences will be good places to start looking for malware.
2. Trend Micro's HiJackThisHiJackThis is Process Explorer on steroids, making the application somewhat daunting to those of us not completely familiar with operating systems. Still, running HiJackThis before having malware problems creates a great reference baseline, making it easy to spot changes. If it's too late to run a baseline scan, do not fear. Several Web sites offer online applications that will automatically analyze the log file from HiJackThis, pointing out possible conflicts. Two that I use are HiJackThis.de Security and NetworkTechs.com. If you would rather have trained experts help, I would recommend WindowSecurity.com's HiJackThis forum.